annotate install_tool_deps.sh @ 0:47ec9c6f44b8 draft

planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
author pjbriggs
date Thu, 09 Nov 2017 10:13:29 -0500
parents
children 1c1902e12caf
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
1 #!/bin/bash -e
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
2 #
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
3 # Install the tool dependencies for Amplicon_analysis_pipeline.sh for
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
4 # testing from command line
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
5 #
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
6 function install_python_package() {
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
7 echo Installing $2 $3 from $4 under $1
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
8 local install_dir=$1
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
9 local install_dirs="$install_dir $install_dir/bin $install_dir/lib/python2.7/site-packages"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
10 for d in $install_dirs ; do
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
11 if [ ! -d $d ] ; then
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
12 mkdir -p $d
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
13 fi
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
14 done
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
15 wd=$(mktemp -d)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
16 echo Moving to $wd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
17 pushd $wd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
18 wget -q $4
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
19 if [ ! -f "$(basename $4)" ] ; then
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
20 echo "No archive $(basename $4)"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
21 exit 1
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
22 fi
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
23 tar xzf $(basename $4)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
24 if [ ! -d "$5" ] ; then
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
25 echo "No directory $5"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
26 exit 1
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
27 fi
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
28 cd $5
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
29 /bin/bash <<EOF
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
30 export PYTHONPATH=$install_dir:$PYTHONPATH && \
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
31 export PYTHONPATH=$install_dir/lib/python2.7/site-packages:$PYTHONPATH && \
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
32 python setup.py install --prefix=$install_dir --install-scripts=$install_dir/bin --install-lib=$install_dir/lib/python2.7/site-packages >>$INSTALL_DIR/INSTALLATION.log 2>&1
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
33 EOF
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
34 popd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
35 rm -rf $wd/*
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
36 rmdir $wd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
37 }
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
38 function install_amplicon_analysis_pipeline_1_1() {
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
39 install_amplicon_analysis_pipeline $1 1.1
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
40 }
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
41 function install_amplicon_analysis_pipeline_1_0() {
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
42 install_amplicon_analysis_pipeline $1 1.0
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
43 }
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
44 function install_amplicon_analysis_pipeline() {
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
45 version=$2
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
46 echo Installing Amplicon_analysis $version
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
47 install_dir=$1/amplicon_analysis_pipeline/$version
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
48 if [ -f $install_dir/env.sh ] ; then
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
49 return
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
50 fi
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
51 mkdir -p $install_dir
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
52 echo Moving to $install_dir
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
53 pushd $install_dir
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
54 wget -q https://github.com/MTutino/Amplicon_analysis/archive/v${version}.tar.gz
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
55 tar zxf v${version}.tar.gz
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
56 mv Amplicon_analysis-${version} Amplicon_analysis
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
57 rm -rf v${version}.tar.gz
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
58 popd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
59 # Make setup file
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
60 cat > $install_dir/env.sh <<EOF
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
61 #!/bin/sh
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
62 # Source this to setup Amplicon_analysis/$version
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
63 echo Setting up Amplicon analysis pipeline $version
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
64 export PATH=$install_dir/Amplicon_analysis:\$PATH
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
65 ## AMPLICON_ANALYSIS_REF_DATA_PATH should be set in
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
66 ## config/local_env.sh or in the job_conf.xml file
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
67 ## - see the README
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
68 ##export AMPLICON_ANALYSIS_REF_DATA_PATH=
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
69 #
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
70 EOF
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
71 }
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
72 function install_amplicon_analysis_pipeline_1_0_patched() {
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
73 version="1.0-patched"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
74 echo Installing Amplicon_analysis $version
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
75 install_dir=$1/amplicon_analysis_pipeline/$version
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
76 if [ -f $install_dir/env.sh ] ; then
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
77 return
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
78 fi
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
79 mkdir -p $install_dir
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
80 echo Moving to $install_dir
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
81 pushd $install_dir
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
82 # Clone and patch analysis pipeline scripts
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
83 git clone https://github.com/pjbriggs/Amplicon_analysis.git
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
84 cd Amplicon_analysis
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
85 git checkout -b $version
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
86 branches=
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
87 if [ ! -z "$branches" ] ; then
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
88 for branch in $branches ; do
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
89 git checkout -b $branch origin/$branch
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
90 git checkout $version
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
91 git merge -m "Merge $branch into $version" $branch
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
92 done
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
93 fi
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
94 cd ..
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
95 popd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
96 # Make setup file
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
97 cat > $install_dir/env.sh <<EOF
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
98 #!/bin/sh
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
99 # Source this to setup Amplicon_analysis/$version
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
100 echo Setting up Amplicon analysis pipeline $version
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
101 export PATH=$install_dir/Amplicon_analysis:\$PATH
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
102 ## AMPLICON_ANALYSIS_REF_DATA_PATH should be set in
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
103 ## config/local_env.sh or in the job_conf.xml file
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
104 ## - see the README
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
105 ##export AMPLICON_ANALYSIS_REF_DATA_PATH=
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
106 #
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
107 EOF
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
108 }
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
109 function install_cutadapt_1_11() {
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
110 echo Installing cutadapt 1.11
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
111 INSTALL_DIR=$1/cutadapt/1.11
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
112 if [ -f $INSTALL_DIR/env.sh ] ; then
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
113 return
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
114 fi
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
115 mkdir -p $INSTALL_DIR
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
116 install_python_package $INSTALL_DIR cutadapt 1.11 \
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
117 https://pypi.python.org/packages/47/bf/9045e90dac084a90aa2bb72c7d5aadefaea96a5776f445f5b5d9a7a2c78b/cutadapt-1.11.tar.gz \
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
118 cutadapt-1.11
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
119 # Make setup file
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
120 cat > $INSTALL_DIR/env.sh <<EOF
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
121 #!/bin/sh
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
122 # Source this to setup cutadapt/1.11
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
123 echo Setting up cutadapt 1.11
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
124 #if [ -f $1/python/2.7.10/env.sh ] ; then
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
125 # . $1/python/2.7.10/env.sh
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
126 #fi
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
127 export PATH=$INSTALL_DIR/bin:\$PATH
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
128 export PYTHONPATH=$INSTALL_DIR:\$PYTHONPATH
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
129 export PYTHONPATH=$INSTALL_DIR/lib:\$PYTHONPATH
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
130 export PYTHONPATH=$INSTALL_DIR/lib/python2.7:\$PYTHONPATH
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
131 export PYTHONPATH=$INSTALL_DIR/lib/python2.7/site-packages:\$PYTHONPATH
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
132 #
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
133 EOF
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
134 }
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
135 function install_sickle_1_33() {
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
136 echo Installing sickle 1.33
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
137 INSTALL_DIR=$1/sickle/1.33
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
138 if [ -f $INSTALL_DIR/env.sh ] ; then
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
139 return
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
140 fi
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
141 mkdir -p $INSTALL_DIR
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
142 mkdir -p $INSTALL_DIR/bin
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
143 wd=$(mktemp -d)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
144 echo Moving to $wd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
145 pushd $wd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
146 wget -q https://github.com/najoshi/sickle/archive/v1.33.tar.gz
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
147 tar zxf v1.33.tar.gz
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
148 cd sickle-1.33
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
149 make >$INSTALL_DIR/INSTALLATION.log 2>&1
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
150 mv sickle $INSTALL_DIR/bin
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
151 popd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
152 rm -rf $wd/*
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
153 rmdir $wd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
154 # Make setup file
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
155 cat > $INSTALL_DIR/env.sh <<EOF
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
156 #!/bin/sh
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
157 # Source this to setup sickle/1.33
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
158 echo Setting up sickle 1.33
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
159 export PATH=$INSTALL_DIR/bin:\$PATH
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
160 #
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
161 EOF
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
162 }
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
163 function install_bioawk_27_08_2013() {
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
164 echo Installing bioawk 27-08-2013
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
165 INSTALL_DIR=$1/bioawk/27-08-2013
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
166 if [ -f $INSTALL_DIR/env.sh ] ; then
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
167 return
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
168 fi
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
169 mkdir -p $INSTALL_DIR
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
170 mkdir -p $INSTALL_DIR/bin
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
171 wd=$(mktemp -d)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
172 echo Moving to $wd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
173 pushd $wd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
174 wget -q https://github.com/lh3/bioawk/archive/v1.0.tar.gz
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
175 tar zxf v1.0.tar.gz
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
176 cd bioawk-1.0
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
177 make >$INSTALL_DIR/INSTALLATION.log 2>&1
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
178 mv bioawk $INSTALL_DIR/bin
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
179 mv maketab $INSTALL_DIR/bin
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
180 popd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
181 rm -rf $wd/*
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
182 rmdir $wd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
183 # Make setup file
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
184 cat > $INSTALL_DIR/env.sh <<EOF
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
185 #!/bin/sh
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
186 # Source this to setup bioawk/2013-07-13
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
187 echo Setting up bioawk 2013-07-13
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
188 export PATH=$INSTALL_DIR/bin:\$PATH
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
189 #
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
190 EOF
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
191 }
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
192 function install_pandaseq_2_8_1() {
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
193 # Taken from https://github.com/fls-bioinformatics-core/galaxy-tools/blob/master/local_dependency_installers/pandaseq.sh
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
194 echo Installing pandaseq 2.8.1
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
195 local install_dir=$1/pandaseq/2.8.1
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
196 if [ -f $install_dir/env.sh ] ; then
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
197 return
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
198 fi
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
199 mkdir -p $install_dir
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
200 local wd=$(mktemp -d)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
201 echo Moving to $wd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
202 pushd $wd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
203 wget -q https://github.com/neufeld/pandaseq/archive/v2.8.1.tar.gz
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
204 tar xzf v2.8.1.tar.gz
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
205 cd pandaseq-2.8.1
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
206 ./autogen.sh >$install_dir/INSTALLATION.log 2>&1
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
207 ./configure --prefix=$install_dir >>$install_dir/INSTALLATION.log 2>&1
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
208 make; make install >>$install_dir/INSTALLATION.log 2>&1
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
209 popd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
210 rm -rf $wd/*
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
211 rmdir $wd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
212 # Make setup file
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
213 cat > $1/pandaseq/2.8.1/env.sh <<EOF
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
214 #!/bin/sh
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
215 # Source this to setup pandaseq/2.8.1
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
216 echo Setting up pandaseq 2.8.1
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
217 export PATH=$install_dir/bin:\$PATH
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
218 export LD_LIBRARY_PATH=$install_dir/lib:\$LD_LIBRARY_PATH
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
219 #
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
220 EOF
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
221 }
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
222 function install_spades_3_5_0() {
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
223 # See http://spades.bioinf.spbau.ru/release3.5.0/manual.html
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
224 echo Installing spades 3.5.0
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
225 local install_dir=$1/spades/3.5.0
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
226 if [ -f $install_dir/env.sh ] ; then
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
227 return
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
228 fi
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
229 mkdir -p $install_dir
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
230 local wd=$(mktemp -d)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
231 echo Moving to $wd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
232 pushd $wd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
233 wget -q http://spades.bioinf.spbau.ru/release3.5.0/SPAdes-3.5.0-Linux.tar.gz
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
234 tar zxf SPAdes-3.5.0-Linux.tar.gz
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
235 cd SPAdes-3.5.0-Linux
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
236 mv bin $install_dir
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
237 mv share $install_dir
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
238 popd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
239 rm -rf $wd/*
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
240 rmdir $wd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
241 # Make setup file
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
242 cat > $1/spades/3.5.0/env.sh <<EOF
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
243 #!/bin/sh
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
244 # Source this to setup spades/3.5.0
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
245 echo Setting up spades 3.5.0
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
246 export PATH=$install_dir/bin:\$PATH
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
247 #
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
248 EOF
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
249 }
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
250 function install_fastqc_0_11_3() {
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
251 echo Installing fastqc 0.11.3
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
252 local install_dir=$1/fastqc/0.11.3
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
253 if [ -f $install_dir/env.sh ] ; then
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
254 return
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
255 fi
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
256 mkdir -p $install_dir
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
257 local wd=$(mktemp -d)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
258 echo Moving to $wd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
259 pushd $wd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
260 wget -q http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.3.zip
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
261 unzip -qq fastqc_v0.11.3.zip
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
262 cd FastQC
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
263 chmod 0755 fastqc
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
264 mv * $install_dir
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
265 popd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
266 rm -rf $wd/*
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
267 rmdir $wd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
268 # Make setup file
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
269 cat > $1/fastqc/0.11.3/env.sh <<EOF
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
270 #!/bin/sh
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
271 # Source this to setup fastqc/0.11.3
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
272 echo Setting up fastqc 0.11.3
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
273 export PATH=$install_dir:\$PATH
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
274 #
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
275 EOF
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
276 }
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
277 function install_qiime_1_8_0() {
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
278 # See http://qiime.org/1.8.0/install/install.html
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
279 echo Installing qiime 1.8.0
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
280 INSTALL_DIR=$1/qiime/1.8.0
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
281 if [ -f $INSTALL_DIR/env.sh ] ; then
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
282 return
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
283 fi
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
284 mkdir -p $INSTALL_DIR
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
285 # Atlas 3.10 (precompiled)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
286 # NB this stolen from galaxyproject/iuc-tools
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
287 local wd=$(mktemp -d)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
288 echo Moving to $wd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
289 pushd $wd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
290 wget -q https://depot.galaxyproject.org/software/atlas/atlas_3.10.2_linux_x64.tar.gz
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
291 tar zxvf atlas_3.10.2_linux_x64.tar.gz
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
292 mv lib $INSTALL_DIR
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
293 command -v gfortran || return 0
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
294 BUNDLED_LGF_CANON=$INSTALL_DIR/lib/libgfortran.so.3.0.0
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
295 BUNDLED_LGF_VERS=`objdump -p $BUNDLED_LGF_CANON | grep GFORTRAN_1 | sed -r 's/.*GFORTRAN_1\.([0-9])+/\1/' | sort -n | tail -1`
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
296 echo 'program test; end program test' > test.f90
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
297 gfortran -o test test.f90
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
298 LGF=`ldd test | grep libgfortran | awk '{print $3}'`
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
299 LGF_CANON=`readlink -f $LGF`
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
300 LGF_VERS=`objdump -p $LGF_CANON | grep GFORTRAN_1 | sed -r 's/.*GFORTRAN_1\.([0-9])+/\1/' | sort -n | tail -1`
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
301 if [ $LGF_VERS -gt $BUNDLED_LGF_VERS ]; then
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
302 cp -p $BUNDLED_LGF_CANON ${BUNDLED_LGF_CANON}.bundled
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
303 cp -p $LGF_CANON $BUNDLED_LGF_CANON
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
304 fi
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
305 popd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
306 rm -rf $wd/*
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
307 rmdir $wd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
308 # Atlas 3.10 (build from source)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
309 # NB this stolen from galaxyproject/iuc-tools
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
310 ##local wd=$(mktemp -d)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
311 ##echo Moving to $wd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
312 ##pushd $wd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
313 ##wget -q https://depot.galaxyproject.org/software/atlas/atlas_3.10.2+gx0_src_all.tar.bz2
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
314 ##wget -q https://depot.galaxyproject.org/software/lapack/lapack_3.5.0_src_all.tar.gz
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
315 ##wget -q https://depot.galaxyproject.org/software/atlas/atlas_patch-blas-lapack-1.0_src_all.diff
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
316 ##wget -q https://depot.galaxyproject.org/software/atlas/atlas_patch-shared-lib-1.0_src_all.diff
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
317 ##wget -q https://depot.galaxyproject.org/software/atlas/atlas_patch-cpu-throttle-1.0_src_all.diff
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
318 ##tar -jxvf atlas_3.10.2+gx0_src_all.tar.bz2
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
319 ##cd ATLAS
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
320 ##mkdir build
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
321 ##patch -p1 < ../atlas_patch-blas-lapack-1.0_src_all.diff
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
322 ##patch -p1 < ../atlas_patch-shared-lib-1.0_src_all.diff
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
323 ##patch -p1 < ../atlas_patch-cpu-throttle-1.0_src_all.diff
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
324 ##cd build
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
325 ##../configure --prefix="$INSTALL_DIR" -D c -DWALL -b 64 -Fa alg '-fPIC' --with-netlib-lapack-tarfile=../../lapack_3.5.0_src_all.tar.gz -v 2 -t 0 -Si cputhrchk 0
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
326 ##make
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
327 ##make install
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
328 ##popd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
329 ##rm -rf $wd/*
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
330 ##rmdir $wd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
331 export ATLAS_LIB_DIR=$INSTALL_DIR/lib
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
332 export ATLAS_INCLUDE_DIR=$INSTALL_DIR/include
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
333 export ATLAS_BLAS_LIB_DIR=$INSTALL_DIR/lib/atlas
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
334 export ATLAS_LAPACK_LIB_DIR=$INSTALL_DIR/lib/atlas
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
335 export ATLAS_ROOT_PATH=$INSTALL_DIR
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
336 export LD_LIBRARY_PATH=$INSTALL_DIR/lib:$LD_LIBRARY_PATH
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
337 export LD_LIBRARY_PATH=$INSTALL_DIR/lib/atlas:$LD_LIBRARY_PATH
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
338 # Numpy 1.7.1
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
339 local wd=$(mktemp -d)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
340 echo Moving to $wd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
341 pushd $wd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
342 wget -q https://depot.galaxyproject.org/software/numpy/numpy_1.7_src_all.tar.gz
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
343 tar -zxvf numpy_1.7_src_all.tar.gz
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
344 cd numpy-1.7.1
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
345 cat > site.cfg <<EOF
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
346 [DEFAULT]
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
347 library_dirs = $ATLAS_LIB_DIR
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
348 include_dirs = $ATLAS_INCLUDE_DIR
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
349 [blas_opt]
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
350 libraries = blas, atlas
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
351 [lapack_opt]
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
352 libraries = lapack, atlas
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
353 EOF
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
354 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python2.7
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
355 export ATLAS=$ATLAS_ROOT_PATH
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
356 python setup.py install --install-lib $INSTALL_DIR/lib/python2.7 --install-scripts $INSTALL_DIR/bin
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
357 popd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
358 rm -rf $wd/*
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
359 rmdir $wd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
360 # Python packages
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
361 ##install_python_package $INSTALL_DIR numpy 1.7.1 \
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
362 ## https://pypi.python.org/packages/84/fb/5e9dfeeb5d8909d659e6892c97c9aa66d3798fad50e1d3d66b3c614a9c35/numpy-1.7.1.tar.gz \
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
363 ## numpy-1.7.1
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
364 install_python_package $INSTALL_DIR matplotlib 1.3.1 \
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
365 https://pypi.python.org/packages/d4/d0/17f17792a4d50994397052220dbe3ac9850ecbde0297b7572933fa4a5c98/matplotlib-1.3.1.tar.gz \
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
366 matplotlib-1.3.1
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
367 install_python_package $INSTALL_DIR qiime 1.8.0 \
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
368 https://github.com/biocore/qiime/archive/1.8.0.tar.gz \
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
369 qiime-1.8.0
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
370 install_python_package $INSTALL_DIR pycogent 1.5.3 \
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
371 https://pypi.python.org/packages/1f/9f/c6f6afe09a3d62a6e809c7745413ffff0f1e8e04d88ab7b56faedf31fe28/cogent-1.5.3.tgz \
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
372 cogent-1.5.3
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
373 install_python_package $INSTALL_DIR pyqi 0.3.1 \
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
374 https://pypi.python.org/packages/60/f0/a7392f5f5caf59a50ccaddbb35a458514953512b7dd6053567cb02849c6e/pyqi-0.3.1.tar.gz \
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
375 pyqi-0.3.1
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
376 install_python_package $INSTALL_DIR biom-format 1.3.1 \
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
377 https://pypi.python.org/packages/98/3b/4e80a9a5c4a3c6764aa8c0c994973e7df71eee02fc6b8cc6e1d06a64ab7e/biom-format-1.3.1.tar.gz \
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
378 biom-format-1.3.1
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
379 install_python_package $INSTALL_DIR qcli 0.1.0 \
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
380 https://pypi.python.org/packages/9a/9a/9c634aed339a5f063e0c954ae439d03b33a7159aa50c6f21034fe2d48fe8/qcli-0.1.0.tar.gz \
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
381 qcli-0.1.0
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
382 install_python_package $INSTALL_DIR pynast 1.2.2 \
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
383 https://pypi.python.org/packages/a0/82/f381ff91afd7a2d92e74c7790823e256d87d5cd0a98c12eaac3d3ec64b8f/pynast-1.2.2.tar.gz \
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
384 pynast-1.2.2
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
385 install_python_package $INSTALL_DIR emperor 0.9.3 \
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
386 https://pypi.python.org/packages/cd/f1/5d502a16a348efe1af7a8d4f41b639c9a165bca0b2f9db36bce89ad1ab40/emperor-0.9.3.tar.gz \
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
387 emperor-0.9.3
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
388 # Update the acceptable Python version
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
389 sed -i 's/acceptable_version = (2,7,3)/acceptable_version = (2,7,6)/g' $INSTALL_DIR/bin/print_qiime_config.py
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
390 # Non-Python dependencies
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
391 local wd=$(mktemp -d)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
392 echo Moving to $wd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
393 pushd $wd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
394 wget -q http://www.microbesonline.org/fasttree/FastTree
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
395 chmod 0755 FastTree
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
396 mv FastTree $INSTALL_DIR/bin
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
397 # Config file
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
398 sed -i 's,qiime_scripts_dir,qiime_scripts_dir\t'"$INSTALL_DIR\/bin"',g' $INSTALL_DIR/lib/python2.7/site-packages/qiime/support_files/qiime_config
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
399 popd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
400 rm -rf $wd/*
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
401 rmdir $wd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
402 # Make setup file
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
403 cat > $INSTALL_DIR/env.sh <<EOF
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
404 #!/bin/sh
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
405 # Source this to setup qiime/1.8.0
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
406 echo Setting up qiime 1.8.0
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
407 #if [ -f $1/python/2.7.10/env.sh ] ; then
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
408 # . $1/python/2.7.10/env.sh
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
409 #fi
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
410 export QIIME_CONFIG_FP=$INSTALL_DIR/lib/python2.7/site-packages/qiime/support_files/qiime_config
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
411 export PATH=$INSTALL_DIR/bin:\$PATH
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
412 export PYTHONPATH=$INSTALL_DIR:\$PYTHONPATH
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
413 export PYTHONPATH=$INSTALL_DIR/lib:\$PYTHONPATH
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
414 export PYTHONPATH=$INSTALL_DIR/lib/python2.7:\$PYTHONPATH
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
415 export PYTHONPATH=$INSTALL_DIR/lib/python2.7/site-packages:\$PYTHONPATH
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
416 export LD_LIBRARY_PATH=$ATLAS_LIB_DIR:\$LD_LIBRARY_PATH
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
417 export LD_LIBRARY_PATH=$ATLAS_LIB_DIR/atlas::\$LD_LIBRARY_PATH
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
418 #
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
419 EOF
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
420 }
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
421 function install_vsearch_1_1_3() {
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
422 echo Installing vsearch 1.1.3
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
423 local install_dir=$1/vsearch/1.1.3
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
424 if [ -f $install_dir/env.sh ] ; then
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
425 return
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
426 fi
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
427 mkdir -p $install_dir/bin
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
428 local wd=$(mktemp -d)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
429 echo Moving to $wd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
430 pushd $wd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
431 wget -q https://github.com/torognes/vsearch/releases/download/v1.1.3/vsearch-1.1.3-linux-x86_64
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
432 chmod 0755 vsearch-1.1.3-linux-x86_64
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
433 mv vsearch-1.1.3-linux-x86_64 $install_dir/bin/vsearch
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
434 ln -s $install_dir/bin/vsearch $install_dir/bin/vsearch113
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
435 popd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
436 # Clean up
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
437 rm -rf $wd/*
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
438 rmdir $wd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
439 # Make setup file
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
440 cat > $install_dir/env.sh <<EOF
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
441 #!/bin/sh
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
442 # Source this to setup vsearch/1.1.3
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
443 echo Setting up vsearch 1.1.3
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
444 export PATH=$install_dir/bin:\$PATH
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
445 #
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
446 EOF
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
447 }
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
448 function install_microbiomeutil_2010_04_29() {
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
449 # Provides ChimeraSlayer
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
450 echo Installing microbiomeutil 2010-04-29
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
451 local install_dir=$1/microbiomeutil/2010-04-29
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
452 if [ -f $install_dir/env.sh ] ; then
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
453 return
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
454 fi
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
455 mkdir -p $install_dir
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
456 local wd=$(mktemp -d)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
457 echo Moving to $wd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
458 pushd $wd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
459 wget -q https://sourceforge.net/projects/microbiomeutil/files/__OLD_VERSIONS/microbiomeutil_2010-04-29.tar.gz
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
460 tar zxf microbiomeutil_2010-04-29.tar.gz
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
461 cd microbiomeutil_2010-04-29
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
462 make >$install_dir/INSTALLATION.log 2>&1
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
463 mv * $install_dir
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
464 popd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
465 # Clean up
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
466 rm -rf $wd/*
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
467 rmdir $wd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
468 # Make setup file
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
469 cat > $install_dir/env.sh <<EOF
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
470 #!/bin/sh
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
471 # Source this to setup microbiomeutil/2010-04-29
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
472 echo Setting up microbiomeutil 2010-04-29
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
473 export PATH=$install_dir/ChimeraSlayer:\$PATH
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
474 #
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
475 EOF
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
476 }
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
477 function install_blast_2_2_26() {
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
478 echo Installing blast 2.2.26
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
479 local install_dir=$1/blast/2.2.26
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
480 if [ -f $install_dir/env.sh ] ; then
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
481 return
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
482 fi
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
483 mkdir -p $install_dir
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
484 local wd=$(mktemp -d)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
485 echo Moving to $wd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
486 pushd $wd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
487 wget -q ftp://ftp.ncbi.nlm.nih.gov/blast/executables/legacy/2.2.26/blast-2.2.26-x64-linux.tar.gz
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
488 tar zxf blast-2.2.26-x64-linux.tar.gz
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
489 cd blast-2.2.26
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
490 mv * $install_dir
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
491 popd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
492 # Clean up
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
493 rm -rf $wd/*
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
494 rmdir $wd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
495 # Make setup file
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
496 cat > $install_dir/env.sh <<EOF
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
497 #!/bin/sh
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
498 # Source this to setup blast/2.2.26
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
499 echo Setting up blast 2.2.26
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
500 export PATH=$install_dir/bin:\$PATH
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
501 #
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
502 EOF
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
503 }
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
504 function install_fasta_number() {
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
505 # See http://drive5.com/python/fasta_number_py.html
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
506 echo Installing fasta_number
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
507 # Install to "default" version i.e. essentially a versionless
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
508 # installation (see Galaxy dependency resolver docs)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
509 local install_dir=$1/fasta_number
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
510 local wd=$(mktemp -d)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
511 echo Moving to $wd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
512 pushd $wd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
513 # Download and use MD5 as local version
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
514 wget -q http://drive5.com/python/python_scripts.tar.gz
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
515 local version=$(md5sum python_scripts.tar.gz | cut -d" " -f1)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
516 # Check for existing installation
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
517 local default_dir=$install_dir/default
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
518 install_dir=$install_dir/$version
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
519 if [ -f $install_dir/env.sh ] ; then
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
520 return
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
521 fi
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
522 # Install scripts and make 'default' link
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
523 mkdir -p $install_dir/bin
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
524 mkdir -p $install_dir/lib
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
525 tar zxf python_scripts.tar.gz
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
526 mv fasta_number.py $install_dir/bin
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
527 mv die.py $install_dir/lib
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
528 ln -s $version $default_dir
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
529 popd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
530 # Clean up
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
531 rm -rf $wd/*
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
532 rmdir $wd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
533 # Make setup file
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
534 cat > $install_dir/env.sh <<EOF
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
535 #!/bin/sh
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
536 # Source this to setup fasta_number/$version
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
537 echo Setting up fasta_number $version
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
538 export PATH=$install_dir/bin:\$PATH
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
539 export PYTHONPATH=$install_dir/lib:\$PYTHONPATH
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
540 #
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
541 EOF
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
542 }
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
543 function install_fasta_splitter_0_2_4() {
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
544 echo Installing fasta-splitter 0.2.4
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
545 local install_dir=$1/fasta-splitter/0.2.4
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
546 if [ -f $install_dir/env.sh ] ; then
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
547 return
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
548 fi
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
549 mkdir -p $install_dir/bin
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
550 local wd=$(mktemp -d)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
551 echo Moving to $wd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
552 pushd $wd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
553 # Install Perl packages using cpanm
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
554 mkdir -p $install_dir/lib/perl5
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
555 wget -q -L https://cpanmin.us/ -O cpanm
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
556 chmod +x cpanm
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
557 for package in "File::Util" ; do
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
558 /bin/bash <<EOF
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
559 export PATH=$install_dir/bin:$PATH PERL5LIB=$install_dir/lib/perl5:$PERL5LIB && \
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
560 ./cpanm -l $install_dir $package >>$install_dir/INSTALLATION.log
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
561 EOF
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
562 done
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
563 # Install fasta-splitter
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
564 wget -q http://kirill-kryukov.com/study/tools/fasta-splitter/files/fasta-splitter-0.2.4.zip
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
565 unzip -qq fasta-splitter-0.2.4.zip
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
566 chmod 0755 fasta-splitter.pl
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
567 mv fasta-splitter.pl $install_dir/bin
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
568 popd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
569 # Clean up
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
570 rm -rf $wd/*
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
571 rmdir $wd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
572 # Make setup file
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
573 cat > $install_dir/env.sh <<EOF
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
574 #!/bin/sh
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
575 # Source this to setup fasta-splitter/0.2.4
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
576 echo Setting up fasta-splitter 0.2.4
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
577 export PATH=$install_dir/bin:\$PATH
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
578 export PERL5LIB=$install_dir/lib/perl5:\$PERL5LIB
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
579 #
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
580 EOF
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
581 }
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
582 function install_rdp_classifier_2_2() {
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
583 echo Installing rdp-classifier 2.2R
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
584 local install_dir=$1/rdp-classifier/2.2
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
585 if [ -f $install_dir/env.sh ] ; then
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
586 return
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
587 fi
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
588 mkdir -p $install_dir
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
589 local wd=$(mktemp -d)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
590 echo Moving to $wd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
591 pushd $wd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
592 wget -q https://sourceforge.net/projects/rdp-classifier/files/rdp-classifier/rdp_classifier_2.2.zip
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
593 unzip -qq rdp_classifier_2.2.zip
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
594 cd rdp_classifier_2.2
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
595 mv * $install_dir
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
596 popd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
597 # Clean up
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
598 rm -rf $wd/*
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
599 rmdir $wd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
600 # Make setup file
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
601 cat > $install_dir/env.sh <<EOF
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
602 #!/bin/sh
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
603 # Source this to setup rdp-classifier/2.2
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
604 echo Setting up RDP classifier 2.2
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
605 export RDP_JAR_PATH=$install_dir/rdp_classifier-2.2.jar
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
606 #
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
607 EOF
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
608 }
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
609 function install_R_3_2_0() {
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
610 # Adapted from https://github.com/fls-bioinformatics-core/galaxy-tools/blob/master/local_dependency_installers/R.sh
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
611 echo Installing R 3.2.0
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
612 local install_dir=$1/R/3.2.0
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
613 if [ -f $install_dir/env.sh ] ; then
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
614 return
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
615 fi
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
616 mkdir -p $install_dir
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
617 local wd=$(mktemp -d)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
618 echo Moving to $wd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
619 pushd $wd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
620 wget -q http://cran.r-project.org/src/base/R-3/R-3.2.0.tar.gz
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
621 tar xzf R-3.2.0.tar.gz
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
622 cd R-3.2.0
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
623 ./configure --prefix=$install_dir
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
624 make
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
625 make install
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
626 popd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
627 # Clean up
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
628 rm -rf $wd/*
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
629 rmdir $wd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
630 # Make setup file
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
631 cat > $install_dir/env.sh <<EOF
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
632 #!/bin/sh
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
633 # Source this to setup R/3.2.0
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
634 echo Setting up R 3.2.0
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
635 export PATH=$install_dir/bin:\$PATH
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
636 export TCL_LIBRARY=$install_dir/lib/libtcl8.4.so
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
637 export TK_LIBRARY=$install_dir/lib/libtk8.4.so
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
638 #
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
639 EOF
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
640 }
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
641 function install_uc2otutab() {
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
642 # See http://drive5.com/python/uc2otutab_py.html
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
643 echo Installing uc2otutab
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
644 # Install to "default" version i.e. essentially a versionless
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
645 # installation (see Galaxy dependency resolver docs)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
646 local install_dir=$1/uc2otutab/default
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
647 if [ -f $install_dir/env.sh ] ; then
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
648 return
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
649 fi
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
650 mkdir -p $install_dir/bin
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
651 local wd=$(mktemp -d)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
652 echo Moving to $wd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
653 pushd $wd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
654 wget -q http://drive5.com/python/python_scripts.tar.gz
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
655 tar zxf python_scripts.tar.gz
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
656 mv die.py fasta.py progress.py uc.py $install_dir/bin
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
657 echo "#!/usr/bin/env python" >$install_dir/bin/uc2otutab.py
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
658 cat uc2otutab.py >>$install_dir/bin/uc2otutab.py
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
659 chmod +x $install_dir/bin/uc2otutab.py
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
660 popd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
661 # Clean up
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
662 rm -rf $wd/*
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
663 rmdir $wd
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
664 # Make setup file
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
665 cat > $install_dir/env.sh <<EOF
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
666 #!/bin/sh
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
667 # Source this to setup uc2otutab/default
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
668 echo Setting up uc2otutab \(default\)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
669 export PATH=$install_dir/bin:\$PATH
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
670 #
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
671 EOF
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
672 }
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
673 ##########################################################
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
674 # Main script starts here
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
675 ##########################################################
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
676 # Fetch top-level installation directory from command line
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
677 TOP_DIR=$1
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
678 if [ -z "$TOP_DIR" ] ; then
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
679 echo Usage: $(basename $0) DIR
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
680 exit
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
681 fi
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
682 if [ -z "$(echo $TOP_DIR | grep ^/)" ] ; then
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
683 TOP_DIR=$(pwd)/$TOP_DIR
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
684 fi
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
685 if [ ! -d "$TOP_DIR" ] ; then
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
686 mkdir -p $TOP_DIR
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
687 fi
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
688 # Install dependencies
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
689 install_amplicon_analysis_pipeline_1_1 $TOP_DIR
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
690 install_cutadapt_1_11 $TOP_DIR
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
691 install_sickle_1_33 $TOP_DIR
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
692 install_bioawk_27_08_2013 $TOP_DIR
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
693 install_pandaseq_2_8_1 $TOP_DIR
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
694 install_spades_3_5_0 $TOP_DIR
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
695 install_fastqc_0_11_3 $TOP_DIR
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
696 install_qiime_1_8_0 $TOP_DIR
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
697 install_vsearch_1_1_3 $TOP_DIR
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
698 install_microbiomeutil_2010_04_29 $TOP_DIR
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
699 install_blast_2_2_26 $TOP_DIR
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
700 install_fasta_number $TOP_DIR
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
701 install_fasta_splitter_0_2_4 $TOP_DIR
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
702 install_rdp_classifier_2_2 $TOP_DIR
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
703 install_R_3_2_0 $TOP_DIR
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
704 install_uc2otutab $TOP_DIR
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
705 ##
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
706 #