# HG changeset patch
# User pjbriggs
# Date 1539868684 14400
# Node ID 3ab198df8f3f86e81e054867cca437144fe1841d
# Parent  43d6f81bc667edc08cd4ae4b599cb2ad5ef4d4aa
planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 15390f18b91d838880d952eb2714f689bbd8a042

diff -r 43d6f81bc667 -r 3ab198df8f3f README.rst
--- a/README.rst	Wed Jun 13 07:45:06 2018 -0400
+++ b/README.rst	Thu Oct 18 09:18:04 2018 -0400
@@ -26,20 +26,8 @@
 instance to detect the dependencies and reference data correctly
 at run time.
 
-1. Install the dependencies
----------------------------
-
-The ``install_tool_deps.sh`` script can be used to fetch and install the
-dependencies locally, for example::
-
-    install_tool_deps.sh /path/to/local_tool_dependencies
-
-This can take some time to complete. When finished it should have
-created a set of directories containing the dependencies under the
-specified top level directory.
-
-2. Install the tool files
--------------------------
+1. Install the tool from the toolshed
+-------------------------------------
 
 The core tool is hosted on the Galaxy toolshed, so it can be installed
 directly from there (this is the recommended route):
@@ -58,7 +46,7 @@
 
     <tool file="Amplicon_analysis/amplicon_analysis_pipeline.xml" />
 
-3. Install the reference data
+2. Install the reference data
 -----------------------------
 
 The script ``References.sh`` from the pipeline package at
@@ -72,33 +60,14 @@
 will install the data in ``/path/to/pipeline/data``.
 
 **NB** The final amount of data downloaded and uncompressed will be
-around 6GB.
-
-4. Configure dependencies and reference data in Galaxy
-------------------------------------------------------
-
-The final steps are to make your Galaxy installation aware of the
-tool dependencies and reference data, so it can locate them both when
-the tool is run.
-
-To target the tool dependencies installed previously, add the
-following lines to the ``dependency_resolvers_conf.xml`` file in the
-Galaxy ``config`` directory::
+around 9GB.
 
-    <dependency_resolvers>
-    ...
-      <galaxy_packages base_path="/path/to/local_tool_dependencies" />
-      <galaxy_packages base_path="/path/to/local_tool_dependencies" versionless="true" />
-      ...
-    </dependency_resolvers>
+3. Configure reference data location in Galaxy
+----------------------------------------------
 
-(NB it is recommended to place these *before* the ``<conda ... />``
-resolvers)
-
-(If you're not familiar with dependency resolvers in Galaxy then
-see the documentation at
-https://docs.galaxyproject.org/en/master/admin/dependency_resolvers.html
-for more details.)
+The final step is to make your Galaxy installation aware of the
+location of the reference data, so it can locate them both when the
+tool is run.
 
 The tool locates the reference data via an environment variable called
 ``AMPLICON_ANALYSIS_REF_DATA_PATH``, which needs to set to the parent
@@ -108,7 +77,8 @@
 installation is configured:
 
  * **For local instances:** add a line to set it in the
-   ``config/local_env.sh`` file of your Galaxy installation, e.g.::
+   ``config/local_env.sh`` file of your Galaxy installation (you
+   may need to create a new empty file first), e.g.::
 
        export AMPLICON_ANALYSIS_REF_DATA_PATH=/path/to/pipeline/data
 
@@ -124,9 +94,9 @@
        <tool id="amplicon_analysis_pipeline" destination="amplicon_analysis"/>
 
    (For more about job destinations see the Galaxy documentation at
-   https://galaxyproject.org/admin/config/jobs/#job-destinations)
+   https://docs.galaxyproject.org/en/master/admin/jobs.html#job-destinations)
 
-5. Enable rendering of HTML outputs from pipeline
+4. Enable rendering of HTML outputs from pipeline
 -------------------------------------------------
 
 To ensure that HTML outputs are displayed correctly in Galaxy
@@ -171,46 +141,32 @@
    https://github.com/galaxyproject/galaxy/issues/4490 and
    https://github.com/galaxyproject/galaxy/issues/1676
 
-Appendix: availability of tool dependencies
-===========================================
-
-The tool takes its dependencies from the underlying pipeline script (see
-https://github.com/MTutino/Amplicon_analysis/blob/master/README.md
-for details).
+Appendix: installing the dependencies manually
+==============================================
 
-As noted above, currently the ``install_tool_deps.sh`` script can be
-used to manually install the dependencies for a local tool install.
+If the tool is installed from the Galaxy toolshed (recommended) then
+the dependencies should be installed automatically and this step can
+be skipped.
 
-In principle these should also be available if the tool were installed
-from a toolshed. However it would be preferrable in this case to get as
-many of the dependencies as possible via the ``conda`` dependency
-resolver.
+Otherwise the ``install_amplicon_analysis_deps.sh`` script can be used
+to fetch and install the dependencies locally, for example::
 
-The following are known to be available via conda, with the required
-version:
+    install_amplicon_analysis.sh /path/to/local_tool_dependencies
 
- - cutadapt 1.8.1
- - sickle-trim 1.33
- - bioawk 1.0
- - fastqc 0.11.3
- - R 3.2.0
-
-Some dependencies are available but with the "wrong" versions:
+(This is the same script as is used to install dependencies from the
+toolshed.) This can take some time to complete, and when completed will
+have created a directory called ``Amplicon_analysis-1.2.3`` containing
+the dependencies under the specified top level directory.
 
- - spades (need 3.5.0)
- - qiime (need 1.8.0)
- - blast (need 2.2.26)
- - vsearch (need 1.1.3)
-
-The following dependencies are currently unavailable:
+**NB** The installed dependencies will occupy around 2.6G of disk
+space.
 
- - fasta_number (need 02jun2015)
- - fasta-splitter (need 0.2.4)
- - rdp_classifier (need 2.2)
- - microbiomeutil (need r20110519)
+You will need to make sure that the ``bin`` subdirectory of this
+directory is on Galaxy's ``PATH`` at runtime, for the tool to be able
+to access the dependencies - for example by adding a line to the
+``local_env.sh`` file like::
 
-(NB usearch 6.1.544 and 8.0.1623 are special cases which must be
-handled outside of Galaxy's dependency management systems.)
+    export PATH=/path/to/local_tool_dependencies/Amplicon_analysis-1.2.3/bin:$PATH
 
 History
 =======
@@ -218,6 +174,8 @@
 ========== ======================================================================
 Version    Changes
 ---------- ----------------------------------------------------------------------
+1.2.3.0    Updated to Amplicon_Analysis_Pipeline version 1.2.3; install
+           dependencies via tool_dependencies.xml.
 1.2.2.0    Updated to Amplicon_Analysis_Pipeline version 1.2.2 (removes
            jackknifed analysis which is not captured by Galaxy tool)
 1.2.1.0    Updated to Amplicon_Analysis_Pipeline version 1.2.1 (adds
diff -r 43d6f81bc667 -r 3ab198df8f3f amplicon_analysis_pipeline.py
--- a/amplicon_analysis_pipeline.py	Wed Jun 13 07:45:06 2018 -0400
+++ b/amplicon_analysis_pipeline.py	Thu Oct 18 09:18:04 2018 -0400
@@ -60,9 +60,10 @@
     sys.stderr.write("%s\n\n" % ('*'*width))
 
 def clean_up_name(sample):
-    # Remove trailing "_L[0-9]+_001" from Fastq
-    # pair names
-    split_name = sample.split('_')
+    # Remove extensions and trailing "_L[0-9]+_001" from
+    # Fastq pair names
+    sample_name = '.'.join(sample.split('.')[:1])
+    split_name = sample_name.split('_')
     if split_name[-1] == "001":
         split_name = split_name[:-1]
     if split_name[-1].startswith('L'):
@@ -139,10 +140,12 @@
 
     # Link to FASTQs and construct Final_name.txt file
     sample_names = []
+    print "-- making Final_name.txt"
     with open("Final_name.txt",'w') as final_name:
         fastqs = iter(args.fastq_pairs)
         for sample_name,fqr1,fqr2 in zip(fastqs,fastqs,fastqs):
             sample_name = clean_up_name(sample_name)
+            print "   %s" % sample_name
             r1 = "%s_R1_.fastq" % sample_name
             r2 = "%s_R2_.fastq" % sample_name
             os.symlink(fqr1,r1)
diff -r 43d6f81bc667 -r 3ab198df8f3f amplicon_analysis_pipeline.xml
--- a/amplicon_analysis_pipeline.xml	Wed Jun 13 07:45:06 2018 -0400
+++ b/amplicon_analysis_pipeline.xml	Thu Oct 18 09:18:04 2018 -0400
@@ -1,21 +1,7 @@
-<tool id="amplicon_analysis_pipeline" name="Amplicon Analysis Pipeline" version="1.2.2.0">
+<tool id="amplicon_analysis_pipeline" name="Amplicon Analysis Pipeline" version="1.2.3.0">
   <description>analyse 16S rRNA data from Illumina Miseq paired-end reads</description>
   <requirements>
-    <requirement type="package" version="1.2.2">amplicon_analysis_pipeline</requirement>
-    <requirement type="package" version="1.11">cutadapt</requirement>
-    <requirement type="package" version="1.33">sickle</requirement>
-    <requirement type="package" version="27-08-2013">bioawk</requirement>
-    <requirement type="package" version="2.8.1">pandaseq</requirement>
-    <requirement type="package" version="3.5.0">spades</requirement>
-    <requirement type="package" version="0.11.3">fastqc</requirement>
-    <requirement type="package" version="1.8.0">qiime</requirement>
-    <requirement type="package" version="2.2.26">blast</requirement>
-    <requirement type="package" version="0.2.4">fasta-splitter</requirement>
-    <requirement type="package" version="2.2">rdp-classifier</requirement>
-    <requirement type="package" version="3.2.0">R</requirement>
-    <requirement type="package" version="1.1.3">vsearch</requirement>
-    <requirement type="package" version="2010-04-29">microbiomeutil</requirement>
-    <requirement type="package">fasta_number</requirement>
+    <requirement type="package" version="1.2.3">amplicon_analysis_pipeline</requirement>
   </requirements>
   <stdio>
     <exit_code range="1:" />
diff -r 43d6f81bc667 -r 3ab198df8f3f install_amplicon_analysis.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/install_amplicon_analysis.sh	Thu Oct 18 09:18:04 2018 -0400
@@ -0,0 +1,425 @@
+#!/bin/sh -e
+#
+# Prototype script to setup a conda environment with the
+# dependencies needed for the Amplicon_analysis_pipeline
+# script
+#
+# Handle command line
+usage()
+{
+    echo "Usage: $(basename $0) [DIR]"
+    echo ""
+    echo "Installs the Amplicon_analysis_pipeline package plus"
+    echo "dependencies in directory DIR (or current directory "
+    echo "if DIR not supplied)"
+}
+if [ ! -z "$1" ] ; then
+    # Check if help was requested
+    case "$1" in
+	--help|-h)
+	    usage
+	    exit 0
+	    ;;
+    esac
+    # Assume it's the installation directory
+    cd $1
+fi
+# Versions
+PIPELINE_VERSION=1.2.3
+RDP_CLASSIFIER_VERSION=2.2
+# Directories
+TOP_DIR=$(pwd)/Amplicon_analysis-${PIPELINE_VERSION}
+BIN_DIR=${TOP_DIR}/bin
+CONDA_DIR=${TOP_DIR}/conda
+CONDA_BIN=${CONDA_DIR}/bin
+CONDA_LIB=${CONDA_DIR}/lib
+CONDA=${CONDA_BIN}/conda
+ENV_NAME="amplicon_analysis_pipeline@${PIPELINE_VERSION}"
+ENV_DIR=${CONDA_DIR}/envs/$ENV_NAME
+#
+# Functions
+#
+# Report failure and terminate script
+fail()
+{
+    echo ""
+    echo ERROR $@ >&2
+    echo ""
+    echo "$(basename $0): installation failed"
+    exit 1
+}
+#
+# Rewrite the shebangs in the installed conda scripts
+# to remove the full path to conda 'bin' directory
+rewrite_conda_shebangs()
+{
+    pattern="s,^#!${CONDA_BIN}/,#!/usr/bin/env ,g"
+    find ${CONDA_BIN} -type f -exec sed -i "$pattern" {} \;
+}
+#
+# Install conda
+install_conda()
+{
+    echo "++++++++++++++++"
+    echo "Installing conda"
+    echo "++++++++++++++++"
+    if [ -e ${CONDA_DIR} ] ; then
+	echo "*** $CONDA_DIR already exists ***" >&2
+	return
+    fi
+    local cwd=$(pwd)
+    local wd=$(mktemp -d)
+    cd $wd
+    wget -q https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
+    bash ./Miniconda2-latest-Linux-x86_64.sh -b -p ${CONDA_DIR}
+    echo Installed conda in ${CONDA_DIR}
+    # Update the installation files
+    # This is to avoid problems when the length the installation
+    # directory path exceeds the limit for the shebang statement
+    # in the conda files
+    echo ""
+    echo -n "Rewriting conda shebangs..."
+    rewrite_conda_shebangs
+    echo "ok"
+    echo -n "Adding conda bin to PATH..."
+    PATH=${CONDA_BIN}:$PATH
+    echo "ok"
+    cd $cwd
+    rm -rf $wd/*
+    rmdir $wd
+}
+#
+# Create conda environment
+install_conda_packages()
+{
+    echo "+++++++++++++++++++++++++"
+    echo "Installing conda packages"
+    echo "+++++++++++++++++++++++++"
+    local cwd=$(pwd)
+    local wd=$(mktemp -d)
+    cd $wd
+    cat >environment.yml <<EOF
+name: ${ENV_NAME}
+channels:
+  - defaults
+  - conda-forge
+  - bioconda
+dependencies:
+  - python=2.7
+  - cutadapt=1.11
+  - sickle-trim=1.33
+  - bioawk=1.0
+  - pandaseq=2.8.1
+  - spades=3.5.0
+  - fastqc=0.11.3
+  - qiime=1.8.0
+  - blast-legacy=2.2.26
+  - fasta-splitter=0.2.4
+  - rdp_classifier=$RDP_CLASSIFIER_VERSION
+  - vsearch=1.1.3
+  # Need to explicitly specify libgfortran
+  # version (otherwise get version incompatible
+  # with numpy=1.7.1)
+  - libgfortran=1.0
+  # Compilers needed to build R
+  - gcc_linux-64
+  - gxx_linux-64
+  - gfortran_linux-64
+EOF
+    ${CONDA} env create --name "${ENV_NAME}" -f environment.yml
+    echo Created conda environment in ${ENV_DIR}
+    cd $cwd
+    rm -rf $wd/*
+    rmdir $wd
+}
+#
+# Install all the non-conda dependencies in a single
+# function (invokes separate functions for each package)
+install_non_conda_packages()
+{
+    echo "+++++++++++++++++++++++++++++"
+    echo "Installing non-conda packages"
+    echo "+++++++++++++++++++++++++++++"
+    # Temporary working directory
+    local wd=$(mktemp -d)
+    local cwd=$(pwd)
+    local wd=$(mktemp -d)
+    cd $wd
+    # Amplicon analysis pipeline
+    echo -n "Installing Amplicon_analysis_pipeline..."
+    if [ -e ${BIN_DIR}/Amplicon_analysis_pipeline.sh ] ; then
+	echo "already installed"
+    else
+	install_amplicon_analysis_pipeline
+	echo "ok"
+    fi
+    # ChimeraSlayer
+    echo -n "Installing ChimeraSlayer..."
+    if [ -e ${BIN_DIR}/ChimeraSlayer.pl ] ; then
+	echo "already installed"
+    else
+	install_chimeraslayer
+	echo "ok"
+    fi
+    # Uclust
+    echo -n "Installing uclust for QIIME/pyNAST..."
+    if [ -e ${BIN_DIR}/uclust ] ; then
+	echo "already installed"
+    else
+	install_uclust
+	echo "ok"
+    fi
+    # R 3.2.1"
+    echo -n "Checking for R 3.2.1..."
+    if [ -e ${BIN_DIR}/R ] ; then
+	echo "R already installed"
+    else
+	echo "not found"
+	install_R_3_2_1
+    fi
+}
+#
+# Amplicon analyis pipeline
+install_amplicon_analysis_pipeline()
+{
+    local wd=$(mktemp -d)
+    local cwd=$(pwd)
+    local wd=$(mktemp -d)
+    cd $wd
+    wget -q https://github.com/MTutino/Amplicon_analysis/archive/v${PIPELINE_VERSION}.tar.gz
+    tar zxf v${PIPELINE_VERSION}.tar.gz
+    cd Amplicon_analysis-${PIPELINE_VERSION}
+    INSTALL_DIR=${TOP_DIR}/share/amplicon_analysis_pipeline-${PIPELINE_VERSION}
+    mkdir -p $INSTALL_DIR
+    ln -s $INSTALL_DIR ${TOP_DIR}/share/amplicon_analysis_pipeline
+    for f in *.sh ; do
+	/bin/cp $f $INSTALL_DIR
+    done
+    /bin/cp -r uc2otutab $INSTALL_DIR
+    mkdir -p ${BIN_DIR}
+    cat >${BIN_DIR}/Amplicon_analysis_pipeline.sh <<EOF
+#!/usr/bin/env bash
+#
+# Point to Qiime config
+export QIIME_CONFIG_FP=${TOP_DIR}/qiime/qiime_config
+# Set up the RDP jar file
+export RDP_JAR_PATH=${TOP_DIR}/share/rdp_classifier/rdp_classifier-${RDP_CLASSIFIER_VERSION}.jar
+# Put the scripts onto the PATH
+export PATH=${BIN_DIR}:${INSTALL_DIR}:\$PATH
+# Activate the conda environment
+export PATH=${CONDA_BIN}:\$PATH
+source ${CONDA_BIN}/activate ${ENV_NAME}
+# Execute the driver script with the supplied arguments
+$INSTALL_DIR/Amplicon_analysis_pipeline.sh \$@
+exit \$?
+EOF
+    chmod 0755 ${BIN_DIR}/Amplicon_analysis_pipeline.sh
+    cat >${BIN_DIR}/install_reference_data.sh <<EOF
+#!/usr/bin/env bash -e
+#
+function usage() {
+  echo "Usage: \$(basename \$0) DIR"
+}
+if [ -z "\$1" ] ; then
+  usage
+  exit 0
+elif [ "\$1" == "--help" ] || [ "\$1" == "-h" ] ; then
+  usage
+  echo ""
+  echo "Install reference data into DIR"
+  exit 0
+fi
+echo "=========================================="
+echo "Installing Amplicon analysis pipeline data"
+echo "=========================================="
+if [ ! -e "\$1" ] ; then
+    echo "Making directory \$1"
+    mkdir -p \$1
+fi
+cd \$1
+DATA_DIR=\$(pwd)
+echo "Installing reference data under \$DATA_DIR"
+$INSTALL_DIR/References.sh
+echo ""
+echo "Use '-r \$DATA_DIR' when running Amplicon_analysis_pipeline.sh"
+echo "to use the reference data from this directory"
+echo ""
+echo "\$(basename \$0): finished"
+EOF
+    chmod 0755 ${BIN_DIR}/install_reference_data.sh
+    cd $cwd
+    rm -rf $wd/*
+    rmdir $wd
+}
+#
+# ChimeraSlayer
+install_chimeraslayer()
+{
+    local cwd=$(pwd)
+    local wd=$(mktemp -d)
+    cd $wd
+    wget -q https://sourceforge.net/projects/microbiomeutil/files/__OLD_VERSIONS/microbiomeutil_2010-04-29.tar.gz
+    tar zxf microbiomeutil_2010-04-29.tar.gz
+    cd microbiomeutil_2010-04-29
+    INSTALL_DIR=${TOP_DIR}/share/microbiome_chimeraslayer-2010-04-29
+    mkdir -p $INSTALL_DIR
+    ln -s $INSTALL_DIR ${TOP_DIR}/share/microbiome_chimeraslayer
+    /bin/cp -r ChimeraSlayer $INSTALL_DIR
+    cat >${BIN_DIR}/ChimeraSlayer.pl <<EOF
+#!/usr/bin/env bash
+export PATH=$INSTALL_DIR:\$PATH
+$INSTALL_DIR/ChimeraSlayer/ChimeraSlayer.pl $@
+EOF
+    chmod 0755 ${INSTALL_DIR}/ChimeraSlayer/ChimeraSlayer.pl
+    chmod 0755 ${BIN_DIR}/ChimeraSlayer.pl
+    cd $cwd
+    rm -rf $wd/*
+    rmdir $wd
+}
+#
+# uclust required for QIIME/pyNAST
+# License only allows this version to be used with those two packages
+# See: http://drive5.com/uclust/downloads1_2_22q.html
+install_uclust()
+{
+    local wd=$(mktemp -d)
+    local cwd=$(pwd)
+    local wd=$(mktemp -d)
+    cd $wd
+    wget -q http://drive5.com/uclust/uclustq1.2.22_i86linux64
+    INSTALL_DIR=${TOP_DIR}/share/uclust-1.2.22
+    mkdir -p $INSTALL_DIR
+    ln -s $INSTALL_DIR ${TOP_DIR}/share/uclust
+    /bin/mv uclustq1.2.22_i86linux64 ${INSTALL_DIR}/uclust
+    chmod 0755 ${INSTALL_DIR}/uclust
+    ln -s  ${INSTALL_DIR}/uclust ${BIN_DIR}
+    cd $cwd
+    rm -rf $wd/*
+    rmdir $wd
+}
+#
+# R 3.2.1
+# Can't use version from conda due to dependency conflicts
+install_R_3_2_1()
+{
+    . ${CONDA_BIN}/activate ${ENV_NAME}
+    local cwd=$(pwd)
+    local wd=$(mktemp -d)
+    cd $wd
+    echo -n "Fetching R 3.2.1 source code..."
+    wget -q http://cran.r-project.org/src/base/R-3/R-3.2.1.tar.gz
+    echo "ok"
+    INSTALL_DIR=${TOP_DIR}
+    mkdir -p $INSTALL_DIR
+    echo -n "Unpacking source code..."
+    tar xzf R-3.2.1.tar.gz >INSTALL.log 2>&1
+    echo "ok"
+    cd R-3.2.1
+    echo -n "Running configure..."
+    ./configure --prefix=$INSTALL_DIR --with-x=no --with-readline=no >>INSTALL.log 2>&1
+    echo "ok"
+    echo -n "Running make..."
+    make >>INSTALL.log 2>&1
+    echo "ok"
+    echo -n "Running make install..."
+    make install >>INSTALL.log 2>&1
+    echo "ok"
+    cd $cwd
+    rm -rf $wd/*
+    rmdir $wd
+    . ${CONDA_BIN}/deactivate
+}
+setup_pipeline_environment()
+{
+    echo "+++++++++++++++++++++++++++++++"
+    echo "Setting up pipeline environment"
+    echo "+++++++++++++++++++++++++++++++"
+    # vsearch113
+    echo -n "Setting up vsearch113..."
+    if [ -e ${BIN_DIR}/vsearch113 ] ; then
+	echo "already exists"
+    elif [ ! -e ${ENV_DIR}/bin/vsearch ] ; then
+	echo "failed"
+	fail "vsearch not found"
+    else
+	ln -s ${ENV_DIR}/bin/vsearch ${BIN_DIR}/vsearch113
+	echo "ok"
+    fi
+    # fasta_splitter.pl
+    echo -n "Setting up fasta_splitter.pl..."
+    if [ -e ${BIN_DIR}/fasta-splitter.pl ] ; then
+	echo "already exists"
+    elif [ ! -e ${ENV_DIR}/share/fasta-splitter/fasta-splitter.pl ] ; then
+	echo "failed"
+	fail "fasta-splitter.pl not found"
+    else
+	ln -s ${ENV_DIR}/share/fasta-splitter/fasta-splitter.pl ${BIN_DIR}/fasta-splitter.pl
+	echo "ok"
+    fi
+    # rdp_classifier.jar
+    local rdp_classifier_jar=rdp_classifier-${RDP_CLASSIFIER_VERSION}.jar
+    echo -n "Setting up rdp_classifier.jar..."
+    if [ -e ${TOP_DIR}/share/rdp_classifier/${rdp_classifier_jar} ] ; then
+	echo "already exists"
+    elif [ ! -e ${ENV_DIR}/share/rdp_classifier/rdp_classifier.jar ] ; then
+	echo "failed"
+	fail "rdp_classifier.jar not found"
+    else
+	mkdir -p ${TOP_DIR}/share/rdp_classifier
+	ln -s ${ENV_DIR}/share/rdp_classifier/rdp_classifier.jar ${TOP_DIR}/share/rdp_classifier/${rdp_classifier_jar}
+	echo "ok"	
+    fi
+    # qiime_config
+    echo -n "Setting up qiime_config..."
+    if [ -e ${TOP_DIR}/qiime/qiime_config ] ; then
+	echo "already exists"
+    else
+	mkdir -p ${TOP_DIR}/qiime
+	cat >${TOP_DIR}/qiime/qiime_config <<EOF-qiime-config
+qiime_scripts_dir	${ENV_DIR}/bin
+EOF-qiime-config
+	echo "ok"
+    fi
+}
+#
+# Remove the compilers from the conda environment
+# Not sure if this step is necessary
+remove_conda_compilers()
+{
+    echo "+++++++++++++++++++++++++++++++++++++++++"
+    echo "Removing compilers from conda environment"
+    echo "+++++++++++++++++++++++++++++++++++++++++"
+    ${CONDA} remove -y -n ${ENV_NAME} gcc_linux-64 gxx_linux-64 gfortran_linux-64
+}
+#
+# Top level script does the installation
+echo "======================================="
+echo "Amplicon_analysis_pipeline installation"
+echo "======================================="
+echo "Installing into ${TOP_DIR}"
+if [ -e ${TOP_DIR} ] ; then
+    fail "Directory already exists"
+fi
+mkdir -p ${TOP_DIR}
+install_conda
+install_conda_packages
+install_non_conda_packages
+setup_pipeline_environment
+remove_conda_compilers
+echo "===================================="
+echo "Amplicon_analysis_pipeline installed"
+echo "===================================="
+echo ""
+echo "Install reference data using:"
+echo ""
+echo "\$ ${BIN_DIR}/install_reference_data.sh DIR"
+echo ""
+echo "Run pipeline scripts using:"
+echo ""
+echo "\$ ${BIN_DIR}/Amplicon_analysis_pipeline.sh ..."
+echo ""
+echo "(or add ${BIN_DIR} to your PATH)"
+echo ""
+echo "$(basename $0): finished"
+##
+#
diff -r 43d6f81bc667 -r 3ab198df8f3f install_tool_deps.sh
--- a/install_tool_deps.sh	Wed Jun 13 07:45:06 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,712 +0,0 @@
-#!/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_2_2() {
-    install_amplicon_analysis_pipeline $1 1.2.2
-}
-function install_amplicon_analysis_pipeline_1_2_1() {
-    install_amplicon_analysis_pipeline $1 1.2.1
-}
-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_2_2 $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
-##
-#
diff -r 43d6f81bc667 -r 3ab198df8f3f tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu Oct 18 09:18:04 2018 -0400
@@ -0,0 +1,16 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <package name="amplicon_analysis_pipeline" version="1.2.3">
+    <install version="1.0">
+      <actions>
+	<action type="download_file">https://raw.githubusercontent.com/pjbriggs/Amplicon_analysis-galaxy/master/install_amplicon_analysis.sh</action>
+	<action type="shell_command">
+	  sh ./install_amplicon_analysis.sh $INSTALL_DIR
+	</action>
+	<action type="set_environment">
+	    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/Amplicon_analysis-1.2.3/bin</environment_variable>
+	</action>
+      </actions>
+    </install>
+  </package>
+</tool_dependency>