--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/install_tool_deps.sh	Thu Nov 09 10:13:29 2017 -0500
@@ -0,0 +1,706 @@
+#!/bin/bash -e
+#
+# Install the tool dependencies for Amplicon_analysis_pipeline.sh for
+# testing from command line
+#
+function install_python_package() {
+    echo Installing $2 $3 from $4 under $1
+    local install_dir=$1
+    local install_dirs="$install_dir $install_dir/bin $install_dir/lib/python2.7/site-packages"
+    for d in $install_dirs ; do
+	if [ ! -d $d ] ; then
+	    mkdir -p $d
+	fi
+    done
+    wd=$(mktemp -d)
+    echo Moving to $wd
+    pushd $wd
+    wget -q $4
+    if [ ! -f "$(basename $4)" ] ; then
+	echo "No archive $(basename $4)"
+	exit 1
+    fi
+    tar xzf $(basename $4)
+    if [ ! -d "$5" ] ; then
+	echo "No directory $5"
+	exit 1
+    fi
+    cd $5
+    /bin/bash <<EOF
+export PYTHONPATH=$install_dir:$PYTHONPATH && \
+export PYTHONPATH=$install_dir/lib/python2.7/site-packages:$PYTHONPATH && \
+python setup.py install --prefix=$install_dir --install-scripts=$install_dir/bin --install-lib=$install_dir/lib/python2.7/site-packages >>$INSTALL_DIR/INSTALLATION.log 2>&1
+EOF
+    popd
+    rm -rf $wd/*
+    rmdir $wd
+}
+function install_amplicon_analysis_pipeline_1_1() {
+    install_amplicon_analysis_pipeline $1 1.1
+}
+function install_amplicon_analysis_pipeline_1_0() {
+    install_amplicon_analysis_pipeline $1 1.0
+}
+function install_amplicon_analysis_pipeline() {
+    version=$2
+    echo Installing Amplicon_analysis $version
+    install_dir=$1/amplicon_analysis_pipeline/$version
+    if [ -f $install_dir/env.sh ] ; then
+	return
+    fi
+    mkdir -p $install_dir
+    echo Moving to $install_dir
+    pushd $install_dir
+    wget -q https://github.com/MTutino/Amplicon_analysis/archive/v${version}.tar.gz
+    tar zxf v${version}.tar.gz
+    mv Amplicon_analysis-${version} Amplicon_analysis
+    rm -rf v${version}.tar.gz
+    popd
+    # Make setup file
+    cat > $install_dir/env.sh <<EOF
+#!/bin/sh
+# Source this to setup Amplicon_analysis/$version
+echo Setting up Amplicon analysis pipeline $version
+export PATH=$install_dir/Amplicon_analysis:\$PATH
+## AMPLICON_ANALYSIS_REF_DATA_PATH should be set in
+## config/local_env.sh or in the job_conf.xml file
+## - see the README
+##export AMPLICON_ANALYSIS_REF_DATA_PATH=
+#
+EOF
+}
+function install_amplicon_analysis_pipeline_1_0_patched() {
+    version="1.0-patched"
+    echo Installing Amplicon_analysis $version
+    install_dir=$1/amplicon_analysis_pipeline/$version
+    if [ -f $install_dir/env.sh ] ; then
+	return
+    fi
+    mkdir -p $install_dir
+    echo Moving to $install_dir
+    pushd $install_dir
+    # Clone and patch analysis pipeline scripts
+    git clone https://github.com/pjbriggs/Amplicon_analysis.git
+    cd Amplicon_analysis
+    git checkout -b $version
+    branches=
+    if [ ! -z "$branches" ] ; then
+	for branch in $branches ; do
+	    git checkout -b $branch origin/$branch
+	    git checkout $version
+	    git merge -m "Merge $branch into $version" $branch
+	done
+    fi
+    cd ..
+    popd
+    # Make setup file
+    cat > $install_dir/env.sh <<EOF
+#!/bin/sh
+# Source this to setup Amplicon_analysis/$version
+echo Setting up Amplicon analysis pipeline $version
+export PATH=$install_dir/Amplicon_analysis:\$PATH
+## AMPLICON_ANALYSIS_REF_DATA_PATH should be set in
+## config/local_env.sh or in the job_conf.xml file
+## - see the README
+##export AMPLICON_ANALYSIS_REF_DATA_PATH=
+#
+EOF
+}
+function install_cutadapt_1_11() {
+    echo Installing cutadapt 1.11
+    INSTALL_DIR=$1/cutadapt/1.11
+    if [ -f $INSTALL_DIR/env.sh ] ; then
+	return
+    fi
+    mkdir -p $INSTALL_DIR
+    install_python_package $INSTALL_DIR cutadapt 1.11 \
+	https://pypi.python.org/packages/47/bf/9045e90dac084a90aa2bb72c7d5aadefaea96a5776f445f5b5d9a7a2c78b/cutadapt-1.11.tar.gz \
+	cutadapt-1.11
+    # Make setup file
+    cat > $INSTALL_DIR/env.sh <<EOF
+#!/bin/sh
+# Source this to setup cutadapt/1.11
+echo Setting up cutadapt 1.11
+#if [ -f $1/python/2.7.10/env.sh ] ; then
+#   . $1/python/2.7.10/env.sh
+#fi
+export PATH=$INSTALL_DIR/bin:\$PATH
+export PYTHONPATH=$INSTALL_DIR:\$PYTHONPATH
+export PYTHONPATH=$INSTALL_DIR/lib:\$PYTHONPATH
+export PYTHONPATH=$INSTALL_DIR/lib/python2.7:\$PYTHONPATH
+export PYTHONPATH=$INSTALL_DIR/lib/python2.7/site-packages:\$PYTHONPATH
+#
+EOF
+}
+function install_sickle_1_33() {
+    echo Installing sickle 1.33
+    INSTALL_DIR=$1/sickle/1.33
+    if [ -f $INSTALL_DIR/env.sh ] ; then
+	return
+    fi
+    mkdir -p $INSTALL_DIR
+    mkdir -p $INSTALL_DIR/bin
+    wd=$(mktemp -d)
+    echo Moving to $wd
+    pushd $wd
+    wget -q https://github.com/najoshi/sickle/archive/v1.33.tar.gz
+    tar zxf v1.33.tar.gz
+    cd sickle-1.33
+    make >$INSTALL_DIR/INSTALLATION.log 2>&1
+    mv sickle $INSTALL_DIR/bin
+    popd
+    rm -rf $wd/*
+    rmdir $wd
+    # Make setup file
+    cat > $INSTALL_DIR/env.sh <<EOF
+#!/bin/sh
+# Source this to setup sickle/1.33
+echo Setting up sickle 1.33
+export PATH=$INSTALL_DIR/bin:\$PATH
+#
+EOF
+}
+function install_bioawk_27_08_2013() {
+    echo Installing bioawk 27-08-2013
+    INSTALL_DIR=$1/bioawk/27-08-2013
+    if [ -f $INSTALL_DIR/env.sh ] ; then
+	return
+    fi
+    mkdir -p $INSTALL_DIR
+    mkdir -p $INSTALL_DIR/bin
+    wd=$(mktemp -d)
+    echo Moving to $wd
+    pushd $wd
+    wget -q https://github.com/lh3/bioawk/archive/v1.0.tar.gz
+    tar zxf v1.0.tar.gz
+    cd bioawk-1.0
+    make >$INSTALL_DIR/INSTALLATION.log 2>&1
+    mv bioawk $INSTALL_DIR/bin
+    mv maketab $INSTALL_DIR/bin
+    popd
+    rm -rf $wd/*
+    rmdir $wd
+    # Make setup file
+    cat > $INSTALL_DIR/env.sh <<EOF
+#!/bin/sh
+# Source this to setup bioawk/2013-07-13
+echo Setting up bioawk 2013-07-13
+export PATH=$INSTALL_DIR/bin:\$PATH
+#
+EOF
+}
+function install_pandaseq_2_8_1() {
+    # Taken from https://github.com/fls-bioinformatics-core/galaxy-tools/blob/master/local_dependency_installers/pandaseq.sh
+    echo Installing pandaseq 2.8.1
+    local install_dir=$1/pandaseq/2.8.1
+    if [ -f $install_dir/env.sh ] ; then
+	return
+    fi
+    mkdir -p $install_dir
+    local wd=$(mktemp -d)
+    echo Moving to $wd
+    pushd $wd
+    wget -q https://github.com/neufeld/pandaseq/archive/v2.8.1.tar.gz
+    tar xzf v2.8.1.tar.gz
+    cd pandaseq-2.8.1
+    ./autogen.sh >$install_dir/INSTALLATION.log 2>&1
+    ./configure --prefix=$install_dir >>$install_dir/INSTALLATION.log 2>&1
+    make; make install >>$install_dir/INSTALLATION.log 2>&1
+    popd
+    rm -rf $wd/*
+    rmdir $wd
+    # Make setup file
+    cat > $1/pandaseq/2.8.1/env.sh <<EOF
+#!/bin/sh
+# Source this to setup pandaseq/2.8.1
+echo Setting up pandaseq 2.8.1
+export PATH=$install_dir/bin:\$PATH
+export LD_LIBRARY_PATH=$install_dir/lib:\$LD_LIBRARY_PATH
+#
+EOF
+}
+function install_spades_3_5_0() {
+    # See http://spades.bioinf.spbau.ru/release3.5.0/manual.html
+    echo Installing spades 3.5.0
+    local install_dir=$1/spades/3.5.0
+    if [ -f $install_dir/env.sh ] ; then
+	return
+    fi
+    mkdir -p $install_dir
+    local wd=$(mktemp -d)
+    echo Moving to $wd
+    pushd $wd
+    wget -q http://spades.bioinf.spbau.ru/release3.5.0/SPAdes-3.5.0-Linux.tar.gz
+    tar zxf SPAdes-3.5.0-Linux.tar.gz
+    cd SPAdes-3.5.0-Linux
+    mv bin $install_dir
+    mv share $install_dir
+    popd
+    rm -rf $wd/*
+    rmdir $wd
+    # Make setup file
+    cat > $1/spades/3.5.0/env.sh <<EOF
+#!/bin/sh
+# Source this to setup spades/3.5.0
+echo Setting up spades 3.5.0
+export PATH=$install_dir/bin:\$PATH
+#
+EOF
+}
+function install_fastqc_0_11_3() {
+    echo Installing fastqc 0.11.3
+    local install_dir=$1/fastqc/0.11.3
+    if [ -f $install_dir/env.sh ] ; then
+	return
+    fi
+    mkdir -p $install_dir
+    local wd=$(mktemp -d)
+    echo Moving to $wd
+    pushd $wd
+    wget -q http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.3.zip
+    unzip -qq fastqc_v0.11.3.zip
+    cd FastQC
+    chmod 0755 fastqc
+    mv * $install_dir
+    popd
+    rm -rf $wd/*
+    rmdir $wd
+    # Make setup file
+    cat > $1/fastqc/0.11.3/env.sh <<EOF
+#!/bin/sh
+# Source this to setup fastqc/0.11.3
+echo Setting up fastqc 0.11.3
+export PATH=$install_dir:\$PATH
+#
+EOF
+}
+function install_qiime_1_8_0() {
+    # See http://qiime.org/1.8.0/install/install.html
+    echo Installing qiime 1.8.0
+    INSTALL_DIR=$1/qiime/1.8.0
+    if [ -f $INSTALL_DIR/env.sh ] ; then
+	return
+    fi
+    mkdir -p $INSTALL_DIR
+    # Atlas 3.10 (precompiled)
+    # NB this stolen from galaxyproject/iuc-tools
+    local wd=$(mktemp -d)
+    echo Moving to $wd
+    pushd $wd
+    wget -q https://depot.galaxyproject.org/software/atlas/atlas_3.10.2_linux_x64.tar.gz
+    tar zxvf atlas_3.10.2_linux_x64.tar.gz
+    mv lib $INSTALL_DIR
+    command -v gfortran || return 0
+    BUNDLED_LGF_CANON=$INSTALL_DIR/lib/libgfortran.so.3.0.0
+    BUNDLED_LGF_VERS=`objdump -p $BUNDLED_LGF_CANON | grep GFORTRAN_1 | sed -r 's/.*GFORTRAN_1\.([0-9])+/\1/' | sort -n | tail -1`
+    echo 'program test; end program test' > test.f90
+    gfortran -o test test.f90
+    LGF=`ldd test | grep libgfortran | awk '{print $3}'`
+    LGF_CANON=`readlink -f $LGF`
+    LGF_VERS=`objdump -p $LGF_CANON | grep GFORTRAN_1 | sed -r 's/.*GFORTRAN_1\.([0-9])+/\1/' | sort -n | tail -1`
+    if [ $LGF_VERS -gt $BUNDLED_LGF_VERS ]; then
+        cp -p $BUNDLED_LGF_CANON ${BUNDLED_LGF_CANON}.bundled
+        cp -p $LGF_CANON $BUNDLED_LGF_CANON
+    fi
+    popd
+    rm -rf $wd/*
+    rmdir $wd
+    # Atlas 3.10 (build from source)
+    # NB this stolen from galaxyproject/iuc-tools
+    ##local wd=$(mktemp -d)
+    ##echo Moving to $wd
+    ##pushd $wd
+    ##wget -q https://depot.galaxyproject.org/software/atlas/atlas_3.10.2+gx0_src_all.tar.bz2
+    ##wget -q https://depot.galaxyproject.org/software/lapack/lapack_3.5.0_src_all.tar.gz
+    ##wget -q https://depot.galaxyproject.org/software/atlas/atlas_patch-blas-lapack-1.0_src_all.diff
+    ##wget -q https://depot.galaxyproject.org/software/atlas/atlas_patch-shared-lib-1.0_src_all.diff
+    ##wget -q https://depot.galaxyproject.org/software/atlas/atlas_patch-cpu-throttle-1.0_src_all.diff
+    ##tar -jxvf atlas_3.10.2+gx0_src_all.tar.bz2
+    ##cd ATLAS
+    ##mkdir build
+    ##patch -p1 < ../atlas_patch-blas-lapack-1.0_src_all.diff
+    ##patch -p1 < ../atlas_patch-shared-lib-1.0_src_all.diff
+    ##patch -p1 < ../atlas_patch-cpu-throttle-1.0_src_all.diff
+    ##cd build
+    ##../configure --prefix="$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
+    ##make
+    ##make install
+    ##popd
+    ##rm -rf $wd/*
+    ##rmdir $wd
+    export ATLAS_LIB_DIR=$INSTALL_DIR/lib
+    export ATLAS_INCLUDE_DIR=$INSTALL_DIR/include
+    export ATLAS_BLAS_LIB_DIR=$INSTALL_DIR/lib/atlas
+    export ATLAS_LAPACK_LIB_DIR=$INSTALL_DIR/lib/atlas
+    export ATLAS_ROOT_PATH=$INSTALL_DIR
+    export LD_LIBRARY_PATH=$INSTALL_DIR/lib:$LD_LIBRARY_PATH
+    export LD_LIBRARY_PATH=$INSTALL_DIR/lib/atlas:$LD_LIBRARY_PATH
+    # Numpy 1.7.1
+    local wd=$(mktemp -d)
+    echo Moving to $wd
+    pushd $wd
+    wget -q https://depot.galaxyproject.org/software/numpy/numpy_1.7_src_all.tar.gz
+    tar -zxvf numpy_1.7_src_all.tar.gz
+    cd numpy-1.7.1
+    cat > site.cfg <<EOF
+[DEFAULT]
+library_dirs = $ATLAS_LIB_DIR
+include_dirs = $ATLAS_INCLUDE_DIR
+[blas_opt]
+libraries = blas, atlas
+[lapack_opt]
+libraries = lapack, atlas
+EOF
+    export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python2.7
+    export ATLAS=$ATLAS_ROOT_PATH
+    python setup.py install --install-lib $INSTALL_DIR/lib/python2.7 --install-scripts $INSTALL_DIR/bin
+    popd
+    rm -rf $wd/*
+    rmdir $wd
+    # Python packages
+    ##install_python_package $INSTALL_DIR numpy 1.7.1 \
+    ## https://pypi.python.org/packages/84/fb/5e9dfeeb5d8909d659e6892c97c9aa66d3798fad50e1d3d66b3c614a9c35/numpy-1.7.1.tar.gz \
+    ## numpy-1.7.1
+    install_python_package $INSTALL_DIR matplotlib 1.3.1 \
+	https://pypi.python.org/packages/d4/d0/17f17792a4d50994397052220dbe3ac9850ecbde0297b7572933fa4a5c98/matplotlib-1.3.1.tar.gz \
+	matplotlib-1.3.1
+    install_python_package $INSTALL_DIR qiime 1.8.0 \
+	https://github.com/biocore/qiime/archive/1.8.0.tar.gz \
+	qiime-1.8.0
+    install_python_package $INSTALL_DIR pycogent 1.5.3 \
+	https://pypi.python.org/packages/1f/9f/c6f6afe09a3d62a6e809c7745413ffff0f1e8e04d88ab7b56faedf31fe28/cogent-1.5.3.tgz \
+	cogent-1.5.3
+    install_python_package $INSTALL_DIR pyqi 0.3.1 \
+	https://pypi.python.org/packages/60/f0/a7392f5f5caf59a50ccaddbb35a458514953512b7dd6053567cb02849c6e/pyqi-0.3.1.tar.gz \
+	pyqi-0.3.1
+    install_python_package $INSTALL_DIR biom-format 1.3.1 \
+	https://pypi.python.org/packages/98/3b/4e80a9a5c4a3c6764aa8c0c994973e7df71eee02fc6b8cc6e1d06a64ab7e/biom-format-1.3.1.tar.gz \
+	biom-format-1.3.1
+    install_python_package $INSTALL_DIR qcli 0.1.0 \
+	https://pypi.python.org/packages/9a/9a/9c634aed339a5f063e0c954ae439d03b33a7159aa50c6f21034fe2d48fe8/qcli-0.1.0.tar.gz \
+	qcli-0.1.0
+    install_python_package $INSTALL_DIR pynast 1.2.2 \
+	https://pypi.python.org/packages/a0/82/f381ff91afd7a2d92e74c7790823e256d87d5cd0a98c12eaac3d3ec64b8f/pynast-1.2.2.tar.gz \
+	pynast-1.2.2
+    install_python_package $INSTALL_DIR emperor 0.9.3 \
+	https://pypi.python.org/packages/cd/f1/5d502a16a348efe1af7a8d4f41b639c9a165bca0b2f9db36bce89ad1ab40/emperor-0.9.3.tar.gz \
+	emperor-0.9.3
+    # Update the acceptable Python version
+    sed -i 's/acceptable_version = (2,7,3)/acceptable_version = (2,7,6)/g' $INSTALL_DIR/bin/print_qiime_config.py
+    # Non-Python dependencies
+    local wd=$(mktemp -d)
+    echo Moving to $wd
+    pushd $wd
+    wget -q http://www.microbesonline.org/fasttree/FastTree
+    chmod 0755 FastTree
+    mv FastTree $INSTALL_DIR/bin
+    # Config file
+    sed -i 's,qiime_scripts_dir,qiime_scripts_dir\t'"$INSTALL_DIR\/bin"',g' $INSTALL_DIR/lib/python2.7/site-packages/qiime/support_files/qiime_config
+    popd
+    rm -rf $wd/*
+    rmdir $wd
+    # Make setup file
+    cat > $INSTALL_DIR/env.sh <<EOF
+#!/bin/sh
+# Source this to setup qiime/1.8.0
+echo Setting up qiime 1.8.0
+#if [ -f $1/python/2.7.10/env.sh ] ; then
+#   . $1/python/2.7.10/env.sh
+#fi
+export QIIME_CONFIG_FP=$INSTALL_DIR/lib/python2.7/site-packages/qiime/support_files/qiime_config
+export PATH=$INSTALL_DIR/bin:\$PATH
+export PYTHONPATH=$INSTALL_DIR:\$PYTHONPATH
+export PYTHONPATH=$INSTALL_DIR/lib:\$PYTHONPATH
+export PYTHONPATH=$INSTALL_DIR/lib/python2.7:\$PYTHONPATH
+export PYTHONPATH=$INSTALL_DIR/lib/python2.7/site-packages:\$PYTHONPATH
+export LD_LIBRARY_PATH=$ATLAS_LIB_DIR:\$LD_LIBRARY_PATH
+export LD_LIBRARY_PATH=$ATLAS_LIB_DIR/atlas::\$LD_LIBRARY_PATH
+#
+EOF
+}
+function install_vsearch_1_1_3() {
+    echo Installing vsearch 1.1.3
+    local install_dir=$1/vsearch/1.1.3
+    if [ -f $install_dir/env.sh ] ; then
+	return
+    fi
+    mkdir -p $install_dir/bin
+    local wd=$(mktemp -d)
+    echo Moving to $wd
+    pushd $wd
+    wget -q https://github.com/torognes/vsearch/releases/download/v1.1.3/vsearch-1.1.3-linux-x86_64
+    chmod 0755 vsearch-1.1.3-linux-x86_64
+    mv vsearch-1.1.3-linux-x86_64 $install_dir/bin/vsearch
+    ln -s $install_dir/bin/vsearch $install_dir/bin/vsearch113
+    popd
+    # Clean up
+    rm -rf $wd/*
+    rmdir $wd
+    # Make setup file
+cat > $install_dir/env.sh <<EOF
+#!/bin/sh
+# Source this to setup vsearch/1.1.3
+echo Setting up vsearch 1.1.3
+export PATH=$install_dir/bin:\$PATH
+#
+EOF
+}
+function install_microbiomeutil_2010_04_29() {
+    # Provides ChimeraSlayer
+    echo Installing microbiomeutil 2010-04-29
+    local install_dir=$1/microbiomeutil/2010-04-29
+    if [ -f $install_dir/env.sh ] ; then
+	return
+    fi
+    mkdir -p $install_dir
+    local wd=$(mktemp -d)
+    echo Moving to $wd
+    pushd $wd
+    wget -q https://sourceforge.net/projects/microbiomeutil/files/__OLD_VERSIONS/microbiomeutil_2010-04-29.tar.gz
+    tar zxf microbiomeutil_2010-04-29.tar.gz
+    cd microbiomeutil_2010-04-29
+    make >$install_dir/INSTALLATION.log 2>&1
+    mv * $install_dir
+    popd
+    # Clean up
+    rm -rf $wd/*
+    rmdir $wd
+    # Make setup file
+cat > $install_dir/env.sh <<EOF
+#!/bin/sh
+# Source this to setup microbiomeutil/2010-04-29
+echo Setting up microbiomeutil 2010-04-29
+export PATH=$install_dir/ChimeraSlayer:\$PATH
+#
+EOF
+}
+function install_blast_2_2_26() {
+    echo Installing blast 2.2.26
+    local install_dir=$1/blast/2.2.26
+    if [ -f $install_dir/env.sh ] ; then
+	return
+    fi
+    mkdir -p $install_dir
+    local wd=$(mktemp -d)
+    echo Moving to $wd
+    pushd $wd
+    wget -q ftp://ftp.ncbi.nlm.nih.gov/blast/executables/legacy/2.2.26/blast-2.2.26-x64-linux.tar.gz
+    tar zxf blast-2.2.26-x64-linux.tar.gz
+    cd blast-2.2.26
+    mv * $install_dir
+    popd
+    # Clean up
+    rm -rf $wd/*
+    rmdir $wd
+    # Make setup file
+cat > $install_dir/env.sh <<EOF
+#!/bin/sh
+# Source this to setup blast/2.2.26
+echo Setting up blast 2.2.26
+export PATH=$install_dir/bin:\$PATH
+#
+EOF
+}
+function install_fasta_number() {
+    # See http://drive5.com/python/fasta_number_py.html
+    echo Installing fasta_number
+    # Install to "default" version i.e. essentially a versionless
+    # installation (see Galaxy dependency resolver docs)
+    local install_dir=$1/fasta_number
+    local wd=$(mktemp -d)
+    echo Moving to $wd
+    pushd $wd
+    # Download and use MD5 as local version
+    wget -q http://drive5.com/python/python_scripts.tar.gz
+    local version=$(md5sum python_scripts.tar.gz | cut -d" " -f1)
+    # Check for existing installation
+    local default_dir=$install_dir/default
+    install_dir=$install_dir/$version
+    if [ -f $install_dir/env.sh ] ; then
+	return
+    fi
+    # Install scripts and make 'default' link
+    mkdir -p $install_dir/bin
+    mkdir -p $install_dir/lib
+    tar zxf python_scripts.tar.gz
+    mv fasta_number.py $install_dir/bin
+    mv die.py $install_dir/lib
+    ln -s $version $default_dir
+    popd
+    # Clean up
+    rm -rf $wd/*
+    rmdir $wd
+    # Make setup file
+cat > $install_dir/env.sh <<EOF
+#!/bin/sh
+# Source this to setup fasta_number/$version
+echo Setting up fasta_number $version
+export PATH=$install_dir/bin:\$PATH
+export PYTHONPATH=$install_dir/lib:\$PYTHONPATH
+#
+EOF
+}
+function install_fasta_splitter_0_2_4() {
+    echo Installing fasta-splitter 0.2.4
+    local install_dir=$1/fasta-splitter/0.2.4
+    if [ -f $install_dir/env.sh ] ; then
+	return
+    fi
+    mkdir -p $install_dir/bin
+    local wd=$(mktemp -d)
+    echo Moving to $wd
+    pushd $wd
+    # Install Perl packages using cpanm
+    mkdir -p $install_dir/lib/perl5
+    wget -q -L https://cpanmin.us/ -O cpanm
+    chmod +x cpanm
+    for package in "File::Util" ; do
+	/bin/bash <<EOF
+export PATH=$install_dir/bin:$PATH PERL5LIB=$install_dir/lib/perl5:$PERL5LIB && \
+./cpanm -l $install_dir $package >>$install_dir/INSTALLATION.log
+EOF
+    done
+    # Install fasta-splitter
+    wget -q http://kirill-kryukov.com/study/tools/fasta-splitter/files/fasta-splitter-0.2.4.zip
+    unzip -qq fasta-splitter-0.2.4.zip
+    chmod 0755 fasta-splitter.pl
+    mv fasta-splitter.pl $install_dir/bin
+    popd
+    # Clean up
+    rm -rf $wd/*
+    rmdir $wd
+    # Make setup file
+cat > $install_dir/env.sh <<EOF
+#!/bin/sh
+# Source this to setup fasta-splitter/0.2.4
+echo Setting up fasta-splitter 0.2.4
+export PATH=$install_dir/bin:\$PATH
+export PERL5LIB=$install_dir/lib/perl5:\$PERL5LIB
+#
+EOF
+}
+function install_rdp_classifier_2_2() {
+    echo Installing rdp-classifier 2.2R
+    local install_dir=$1/rdp-classifier/2.2
+    if [ -f $install_dir/env.sh ] ; then
+	return
+    fi
+    mkdir -p $install_dir
+    local wd=$(mktemp -d)
+    echo Moving to $wd
+    pushd $wd
+    wget -q https://sourceforge.net/projects/rdp-classifier/files/rdp-classifier/rdp_classifier_2.2.zip
+    unzip -qq rdp_classifier_2.2.zip
+    cd rdp_classifier_2.2
+    mv * $install_dir
+    popd
+    # Clean up
+    rm -rf $wd/*
+    rmdir $wd
+    # Make setup file
+cat > $install_dir/env.sh <<EOF
+#!/bin/sh
+# Source this to setup rdp-classifier/2.2
+echo Setting up RDP classifier 2.2
+export RDP_JAR_PATH=$install_dir/rdp_classifier-2.2.jar
+#
+EOF
+}
+function install_R_3_2_0() {
+    # Adapted from https://github.com/fls-bioinformatics-core/galaxy-tools/blob/master/local_dependency_installers/R.sh
+    echo Installing R 3.2.0
+    local install_dir=$1/R/3.2.0
+    if [ -f $install_dir/env.sh ] ; then
+	return
+    fi
+    mkdir -p $install_dir
+    local wd=$(mktemp -d)
+    echo Moving to $wd
+    pushd $wd
+    wget -q http://cran.r-project.org/src/base/R-3/R-3.2.0.tar.gz
+    tar xzf R-3.2.0.tar.gz
+    cd R-3.2.0
+    ./configure --prefix=$install_dir
+    make
+    make install
+    popd
+    # Clean up
+    rm -rf $wd/*
+    rmdir $wd
+    # Make setup file
+cat > $install_dir/env.sh <<EOF
+#!/bin/sh
+# Source this to setup R/3.2.0
+echo Setting up R 3.2.0
+export PATH=$install_dir/bin:\$PATH
+export TCL_LIBRARY=$install_dir/lib/libtcl8.4.so
+export TK_LIBRARY=$install_dir/lib/libtk8.4.so
+#
+EOF
+}
+function install_uc2otutab() {
+    # See http://drive5.com/python/uc2otutab_py.html
+    echo Installing uc2otutab
+    # Install to "default" version i.e. essentially a versionless
+    # installation (see Galaxy dependency resolver docs)
+    local install_dir=$1/uc2otutab/default
+    if [ -f $install_dir/env.sh ] ; then
+	return
+    fi
+    mkdir -p $install_dir/bin
+    local wd=$(mktemp -d)
+    echo Moving to $wd
+    pushd $wd
+    wget -q http://drive5.com/python/python_scripts.tar.gz
+    tar zxf python_scripts.tar.gz
+    mv die.py fasta.py progress.py uc.py $install_dir/bin
+    echo "#!/usr/bin/env python" >$install_dir/bin/uc2otutab.py
+    cat uc2otutab.py >>$install_dir/bin/uc2otutab.py
+    chmod +x $install_dir/bin/uc2otutab.py
+    popd
+    # Clean up
+    rm -rf $wd/*
+    rmdir $wd
+    # Make setup file
+cat > $install_dir/env.sh <<EOF
+#!/bin/sh
+# Source this to setup uc2otutab/default
+echo Setting up uc2otutab \(default\)
+export PATH=$install_dir/bin:\$PATH
+#
+EOF
+}
+##########################################################
+# Main script starts here
+##########################################################
+# Fetch top-level installation directory from command line
+TOP_DIR=$1
+if [ -z "$TOP_DIR" ] ; then
+    echo Usage: $(basename $0) DIR
+    exit
+fi
+if [ -z "$(echo $TOP_DIR | grep ^/)" ] ; then
+    TOP_DIR=$(pwd)/$TOP_DIR
+fi
+if [ ! -d "$TOP_DIR" ] ; then
+    mkdir -p $TOP_DIR
+fi
+# Install dependencies
+install_amplicon_analysis_pipeline_1_1 $TOP_DIR
+install_cutadapt_1_11 $TOP_DIR
+install_sickle_1_33 $TOP_DIR
+install_bioawk_27_08_2013 $TOP_DIR
+install_pandaseq_2_8_1 $TOP_DIR
+install_spades_3_5_0 $TOP_DIR
+install_fastqc_0_11_3 $TOP_DIR
+install_qiime_1_8_0 $TOP_DIR
+install_vsearch_1_1_3 $TOP_DIR
+install_microbiomeutil_2010_04_29 $TOP_DIR
+install_blast_2_2_26 $TOP_DIR
+install_fasta_number $TOP_DIR
+install_fasta_splitter_0_2_4 $TOP_DIR
+install_rdp_classifier_2_2 $TOP_DIR
+install_R_3_2_0 $TOP_DIR
+install_uc2otutab $TOP_DIR
+##
+#