# HG changeset patch
# User pjbriggs
# Date 1510240409 18000
# Node ID 47ec9c6f44b8be9984fd6ec487574cf15b684dc5

planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92

diff -r 000000000000 -r 47ec9c6f44b8 README.rst
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Thu Nov 09 10:13:29 2017 -0500
@@ -0,0 +1,249 @@
+Amplicon_analysis-galaxy
+========================
+
+A Galaxy tool wrapper to Mauro Tutino's ``Amplicon_analysis`` pipeline
+script at https://github.com/MTutino/Amplicon_analysis
+
+The pipeline can analyse paired-end 16S rRNA data from Illumina Miseq
+(Casava >= 1.8) and performs the following operations:
+
+ * QC and clean up of input data
+ * Removal of singletons and chimeras and building of OTU table
+   and phylogenetic tree
+ * Beta and alpha diversity of analysis
+
+Usage documentation
+===================
+
+Usage of the tool (including required inputs) is documented within
+the ``help`` section of the tool XML.
+
+Installing the tool in a Galaxy instance
+========================================
+
+The following sections describe how to install the tool files,
+dependencies and reference data, and how to configure the Galaxy
+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
+-------------------------
+
+The core tool is hosted on the Galaxy toolshed, so it can be installed
+directly from there (this is the recommended route):
+
+ * https://toolshed.g2.bx.psu.edu/view/pjbriggs/amplicon_analysis_pipeline/
+
+Alternatively it can be installed manually; in this case there are two
+files to install:
+
+ * ``amplicon_analysis_pipeline.xml`` (the Galaxy tool definition)
+ * ``amplicon_analysis_pipeline.py`` (the Python wrapper script)
+
+Put these in a directory that is visible to Galaxy (e.g. a
+``tools/Amplicon_analysis/`` folder), and modify the ``tools_conf.xml``
+file to tell Galaxy to offer the tool by adding the line e.g.::
+
+    <tool file="Amplicon_analysis/amplicon_analysis_pipeline.xml" />
+
+3. Install the reference data
+-----------------------------
+
+The script ``References.sh`` from the pipeline package at
+https://github.com/MTutino/Amplicon_analysis can be run to install
+the reference data, for example::
+
+    cd /path/to/pipeline/data
+    wget https://github.com/MTutino/Amplicon_analysis/raw/master/References.sh
+    /bin/bash ./References.sh
+
+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::
+
+    <dependency_resolvers>
+    ...
+      <galaxy_packages base_path="/path/to/local_tool_dependencies" />
+      <galaxy_packages base_path="/path/to/local_tool_dependencies" versionless="true" />
+      ...
+    </dependency_resolvers>
+
+(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 tool locates the reference data via an environment variable called
+``AMPLICON_ANALYSIS_REF_DATA_PATH``, which needs to set to the parent
+directory where the reference data has been installed.
+
+There are various ways to do this, depending on how your Galaxy
+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.::
+
+       export AMPLICON_ANALYSIS_REF_DATA_PATH=/path/to/pipeline/data
+
+ * **For production instances:** set the value in the ``job_conf.xml``
+   configuration file, e.g.::
+
+       <destination id="amplicon_analysis">
+          <env id="AMPLICON_ANALYSIS_REF_DATA_PATH">/path/to/pipeline/data</env>
+       </destination>
+
+   and then specify that the pipeline tool uses this destination::
+
+       <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)
+
+5. Enable rendering of HTML outputs from pipeline
+-------------------------------------------------
+
+To ensure that HTML outputs are displayed correctly in Galaxy
+(for example the Vsearch OTU table heatmaps), Galaxy needs to be
+configured not to sanitize the outputs from the ``Amplicon_analysis``
+tool.
+
+Either:
+
+ * **For local instances:** set ``sanitize_all_html = False`` in
+   ``config/galaxy.ini`` (nb don't do this on production servers or
+   public instances!); or
+
+ * **For production instances:** add the ``Amplicon_analysis`` tool
+   to the display whitelist in the Galaxy instance:
+
+   - Set ``sanitize_whitelist_file = config/whitelist.txt`` in
+     ``config/galaxy.ini`` and restart Galaxy;
+   - Go to ``Admin>Manage Display Whitelist``, check the box for
+     ``Amplicon_analysis`` (hint: use your browser's 'find-in-page'
+     search function to help locate it) and click on
+     ``Submit new whitelist`` to update the settings.
+
+Additional details
+==================
+
+Some other things to be aware of:
+
+ * Note that using the Silva database requires a minimum of 18Gb RAM
+
+Known problems
+==============
+
+ * Only the ``VSEARCH`` pipeline in Mauro's script is currently
+   available via the Galaxy tool; the ``USEARCH`` and ``QIIME``
+   pipelines have yet to be implemented.
+ * The images in the tool help section are not visible if the
+   tool has been installed locally, or if it has been installed in
+   a Galaxy instance which is served from a subdirectory.
+
+   These are both problems with Galaxy and not the tool, see
+   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).
+
+As noted above, currently the ``install_tool_deps.sh`` script can be
+used to manually install the dependencies for a local tool install.
+
+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.
+
+The following are known to be available via conda, with the required
+version:
+
+ - 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:
+
+ - 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:
+
+ - fasta_number (need 02jun2015)
+ - fasta-splitter (need 0.2.4)
+ - rdp_classifier (need 2.2)
+ - microbiomeutil (need r20110519)
+
+(NB usearch 6.1.544 and 8.0.1623 are special cases which must be
+handled outside of Galaxy's dependency management systems.)
+
+History
+=======
+
+========== ======================================================================
+Version    Changes
+---------- ----------------------------------------------------------------------
+1.1.0      First official version on Galaxy toolshed.
+1.0.6      Expand inline documentation to provide detailed usage guidance.
+1.0.5      Updates including:
+
+           - Capture read counts from quality control as new output dataset
+           - Capture FastQC per-base quality boxplots for each sample as
+             new output dataset
+           - Add support for -l option (sliding window length for trimming)
+           - Default for -L set to "200"
+1.0.4      Various updates:
+
+	   - Additional outputs are captured when a "Categories" file is
+	     supplied (alpha diversity rarefaction curves and boxplots)
+	   - Sample names derived from Fastqs in a collection of pairs
+	     are trimmed to SAMPLE_S* (for Illumina-style Fastq filenames)
+           - Input Fastqs can now be of more general ``fastq`` type
+	   - Log file outputs are captured in new output dataset
+	   - User can specify a "title" for the job which is copied into
+	     the dataset names (to distinguish outputs from different runs)
+	   - Improved detection and reporting of problems with input
+	     Metatable
+1.0.3      Take the sample names from the collection dataset names when
+           using collection as input (this is now the default input mode);
+           collect additional output dataset; disable ``usearch``-based
+           pipelines (i.e. ``UPARSE`` and ``QIIME``).
+1.0.2      Enable support for FASTQs supplied via dataset collections and
+           fix some broken output datasets.
+1.0.1      Initial version
+========== ======================================================================
diff -r 000000000000 -r 47ec9c6f44b8 amplicon_analysis_pipeline.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/amplicon_analysis_pipeline.py	Thu Nov 09 10:13:29 2017 -0500
@@ -0,0 +1,329 @@
+#!/usr/bin/env python
+#
+# Wrapper script to run Amplicon_analysis_pipeline.sh
+# from Galaxy tool
+
+import sys
+import os
+import argparse
+import subprocess
+import glob
+
+class PipelineCmd(object):
+    def __init__(self,cmd):
+        self.cmd = [str(cmd)]
+    def add_args(self,*args):
+        for arg in args:
+            self.cmd.append(str(arg))
+    def __repr__(self):
+        return ' '.join([str(arg) for arg in self.cmd])
+
+def ahref(target,name=None,type=None):
+    if name is None:
+        name = os.path.basename(target)
+    ahref = "<a href='%s'" % target
+    if type is not None:
+        ahref += " type='%s'" % type
+    ahref += ">%s</a>" % name
+    return ahref
+
+def check_errors():
+    # Errors in Amplicon_analysis_pipeline.log
+    with open('Amplicon_analysis_pipeline.log','r') as pipeline_log:
+        log = pipeline_log.read()
+        if "Names in the first column of Metatable.txt and in the second column of Final_name.txt do not match" in log:
+            print_error("""*** Sample IDs don't match dataset names ***
+
+The sample IDs (first column of the Metatable file) don't match the
+supplied sample names for the input Fastq pairs.
+""")
+    # Errors in pipeline output
+    with open('pipeline.log','r') as pipeline_log:
+        log = pipeline_log.read()
+        if "Errors and/or warnings detected in mapping file" in log:
+            with open("Metatable_log/Metatable.log","r") as metatable_log:
+                # Echo the Metatable log file to the tool log
+                print_error("""*** Error in Metatable mapping file ***
+
+%s""" % metatable_log.read())
+        elif "No header line was found in mapping file" in log:
+            # Report error to the tool log
+            print_error("""*** No header in Metatable mapping file ***
+
+Check you've specified the correct file as the input Metatable""")
+
+def print_error(message):
+    width = max([len(line) for line in message.split('\n')]) + 4
+    sys.stderr.write("\n%s\n" % ('*'*width))
+    for line in message.split('\n'):
+        sys.stderr.write("* %s%s *\n" % (line,' '*(width-len(line)-4)))
+    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('_')
+    if split_name[-1] == "001":
+        split_name = split_name[:-1]
+    if split_name[-1].startswith('L'):
+        try:
+            int(split_name[-1][1:])
+            split_name = split_name[:-1]
+        except ValueError:
+            pass
+    return '_'.join(split_name)
+
+def list_outputs(filen=None):
+    # List the output directory contents
+    # If filen is specified then will be the filename to
+    # write to, otherwise write to stdout
+    if filen is not None:
+        fp = open(filen,'w')
+    else:
+        fp = sys.stdout
+    results_dir = os.path.abspath("RESULTS")
+    fp.write("Listing contents of output dir %s:\n" % results_dir)
+    ix = 0
+    for d,dirs,files in os.walk(results_dir):
+        ix += 1
+        fp.write("-- %d: %s\n" % (ix,
+                                  os.path.relpath(d,results_dir)))
+        for f in files:
+            ix += 1
+            fp.write("---- %d: %s\n" % (ix,
+                                        os.path.relpath(f,results_dir)))
+    # Close output file
+    if filen is not None:
+        fp.close()
+
+if __name__ == "__main__":
+    # Command line
+    print "Amplicon analysis: starting"
+    p = argparse.ArgumentParser()
+    p.add_argument("metatable",
+                   metavar="METATABLE_FILE",
+                   help="Metatable.txt file")
+    p.add_argument("fastq_pairs",
+                   metavar="SAMPLE_NAME FQ_R1 FQ_R2",
+                   nargs="+",
+                   default=list(),
+                   help="Triplets of SAMPLE_NAME followed by "
+                   "a R1/R2 FASTQ file pair")
+    p.add_argument("-g",dest="forward_pcr_primer")
+    p.add_argument("-G",dest="reverse_pcr_primer")
+    p.add_argument("-q",dest="trimming_threshold")
+    p.add_argument("-O",dest="minimum_overlap")
+    p.add_argument("-L",dest="minimum_length")
+    p.add_argument("-l",dest="sliding_window_length")
+    p.add_argument("-P",dest="pipeline",
+                   choices=["vsearch","uparse","qiime"],
+                   type=str.lower,
+                   default="vsearch")
+    p.add_argument("-S",dest="use_silva",action="store_true")
+    p.add_argument("-r",dest="reference_data_path")
+    p.add_argument("-c",dest="categories_file")
+    args = p.parse_args()
+
+    # Build the environment for running the pipeline
+    print "Amplicon analysis: building the environment"
+    metatable_file = os.path.abspath(args.metatable)
+    os.symlink(metatable_file,"Metatable.txt")
+    print "-- made symlink to Metatable.txt"
+
+    # Link to Categories.txt file (if provided)
+    if args.categories_file is not None:
+        categories_file = os.path.abspath(args.categories_file)
+        os.symlink(categories_file,"Categories.txt")
+        print "-- made symlink to Categories.txt"
+
+    # Link to FASTQs and construct Final_name.txt file
+    sample_names = []
+    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)
+            r1 = "%s_R1_.fastq" % sample_name
+            r2 = "%s_R2_.fastq" % sample_name
+            os.symlink(fqr1,r1)
+            os.symlink(fqr2,r2)
+            final_name.write("%s\n" % '\t'.join((r1,sample_name)))
+            final_name.write("%s\n" % '\t'.join((r2,sample_name)))
+            sample_names.append(sample_name)
+
+    # Construct the pipeline command
+    print "Amplicon analysis: constructing pipeline command"
+    pipeline = PipelineCmd("Amplicon_analysis_pipeline.sh")
+    if args.forward_pcr_primer:
+        pipeline.add_args("-g",args.forward_pcr_primer)
+    if args.reverse_pcr_primer:
+        pipeline.add_args("-G",args.reverse_pcr_primer)
+    if args.trimming_threshold:
+        pipeline.add_args("-q",args.trimming_threshold)
+    if args.minimum_overlap:
+        pipeline.add_args("-O",args.minimum_overlap)
+    if args.minimum_length:
+        pipeline.add_args("-L",args.minimum_length)
+    if args.sliding_window_length:
+        pipeline.add_args("-l",args.sliding_window_length)
+    if args.reference_data_path:
+        pipeline.add_args("-r",args.reference_data_path)
+    pipeline.add_args("-P",args.pipeline)
+    if args.use_silva:
+        pipeline.add_args("-S")
+
+    # Echo the pipeline command to stdout
+    print "Running %s" % pipeline
+
+    # Run the pipeline
+    with open("pipeline.log","w") as pipeline_out:
+        try:
+            subprocess.check_call(pipeline.cmd,
+                                  stdout=pipeline_out,
+                                  stderr=subprocess.STDOUT)
+            exit_code = 0
+            print "Pipeline completed ok"
+        except subprocess.CalledProcessError as ex:
+            # Non-zero exit status
+            sys.stderr.write("Pipeline failed: exit code %s\n" %
+                             ex.returncode)
+            exit_code = ex.returncode
+        except Exception as ex:
+            # Some other problem
+            sys.stderr.write("Unexpected error: %s\n" % str(ex))
+
+    # Write out the list of outputs
+    outputs_file = "Pipeline_outputs.txt"
+    list_outputs(outputs_file)
+
+    # Check for log file
+    log_file = "Amplicon_analysis_pipeline.log"
+    if os.path.exists(log_file):
+        print "Found log file: %s" % log_file
+        if exit_code == 0:
+            # Create an HTML file to link to log files etc
+            # NB the paths to the files should be correct once
+            # copied by Galaxy on job completion
+            with open("pipeline_outputs.html","w") as html_out:
+                html_out.write("""<html>
+<head>
+<title>Amplicon analysis pipeline: log files</title>
+<head>
+<body>
+<h1>Amplicon analysis pipeline: log files</h1>
+<ul>
+""")
+                html_out.write(
+                    "<li>%s</li>\n" %
+                    ahref("Amplicon_analysis_pipeline.log",
+                          type="text/plain"))
+                html_out.write(
+                    "<li>%s</li>\n" %
+                    ahref("pipeline.log",type="text/plain"))
+                html_out.write(
+                    "<li>%s</li>\n" %
+                    ahref("Pipeline_outputs.txt",
+                          type="text/plain"))
+                html_out.write(
+                    "<li>%s</li>\n" %
+                    ahref("Metatable.html"))
+                html_out.write("""<ul>
+</body>
+</html>
+""")
+        else:
+            # Check for known error messages
+            check_errors()
+            # Write pipeline stdout to tool stderr
+            sys.stderr.write("\nOutput from pipeline:\n")
+            with open("pipeline.log",'r') as log:
+                sys.stderr.write("%s" % log.read())
+            # Write log file contents to tool log
+            print "\nAmplicon_analysis_pipeline.log:"
+            with open(log_file,'r') as log:
+                print "%s" % log.read()
+    else:
+        sys.stderr.write("ERROR missing log file \"%s\"\n" %
+                         log_file)
+
+    # Handle FastQC boxplots
+    print "Amplicon analysis: collating per base quality boxplots"
+    with open("fastqc_quality_boxplots.html","w") as quality_boxplots:
+        # PHRED value for trimming
+        phred_score = 20
+        if args.trimming_threshold is not None:
+            phred_score = args.trimming_threshold
+        # Write header for HTML output file
+        quality_boxplots.write("""<html>
+<head>
+<title>Amplicon analysis pipeline: Per-base Quality Boxplots (FastQC)</title>
+<head>
+<body>
+<h1>Amplicon analysis pipeline: Per-base Quality Boxplots (FastQC)</h1>
+""")
+        # Look for raw and trimmed FastQC output for each sample
+        for sample_name in sample_names:
+            fastqc_dir = os.path.join(sample_name,"FastQC")
+            quality_boxplots.write("<h2>%s</h2>" % sample_name)
+            for d in ("Raw","cutdapt_sickle/Q%s" % phred_score):
+                quality_boxplots.write("<h3>%s</h3>" % d)
+                fastqc_html_files = glob.glob(
+                    os.path.join(fastqc_dir,d,"*_fastqc.html"))
+                if not fastqc_html_files:
+                    quality_boxplots.write("<p>No FastQC outputs found</p>")
+                    continue
+                # Pull out the per-base quality boxplots
+                for f in fastqc_html_files:
+                    boxplot = None
+                    with open(f) as fp:
+                        for line in fp.read().split(">"):
+                            try:
+                                line.index("alt=\"Per base quality graph\"")
+                                boxplot = line + ">"
+                                break
+                            except ValueError:
+                                pass
+                    if boxplot is None:
+                        boxplot = "Missing plot"
+                    quality_boxplots.write("<h4>%s</h4><p>%s</p>" %
+                                           (os.path.basename(f),
+                                            boxplot))
+            quality_boxplots.write("""</body>
+</html>
+""")
+
+    # Handle additional output when categories file was supplied
+    if args.categories_file is not None:
+        # Alpha diversity boxplots
+        print "Amplicon analysis: indexing alpha diversity boxplots"
+        boxplots_dir = os.path.abspath(
+            os.path.join("RESULTS",
+                         "%s_%s" % (args.pipeline.title(),
+                                    ("gg" if not args.use_silva
+                                     else "silva")),
+                         "Alpha_diversity",
+                         "Alpha_diversity_boxplot",
+                         "Categories_shannon"))
+        print "Amplicon analysis: gathering PDFs from %s" % boxplots_dir
+        boxplot_pdfs = [os.path.basename(pdf)
+                        for pdf in
+                        sorted(glob.glob(
+                            os.path.join(boxplots_dir,"*.pdf")))]
+        with open("alpha_diversity_boxplots.html","w") as boxplots_out:
+            boxplots_out.write("""<html>
+<head>
+<title>Amplicon analysis pipeline: Alpha Diversity Boxplots (Shannon)</title>
+<head>
+<body>
+<h1>Amplicon analysis pipeline: Alpha Diversity Boxplots (Shannon)</h1>
+""")
+            boxplots_out.write("<ul>\n")
+            for pdf in boxplot_pdfs:
+                boxplots_out.write("<li>%s</li>\n" % ahref(pdf))
+            boxplots_out.write("<ul>\n")
+            boxplots_out.write("""</body>
+</html>
+""")
+
+    # Finish
+    print "Amplicon analysis: finishing, exit code: %s" % exit_code
+    sys.exit(exit_code)
diff -r 000000000000 -r 47ec9c6f44b8 amplicon_analysis_pipeline.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/amplicon_analysis_pipeline.xml	Thu Nov 09 10:13:29 2017 -0500
@@ -0,0 +1,484 @@
+<tool id="amplicon_analysis_pipeline" name="Amplicon Analysis Pipeline" version="1.0.6">
+  <description>analyse 16S rRNA data from Illumina Miseq paired-end reads</description>
+  <requirements>
+    <requirement type="package" version="1.1">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>
+  </requirements>
+  <stdio>
+    <exit_code range="1:" />
+  </stdio>
+  <command><![CDATA[
+  ## Set the reference database name
+  #if $reference_database == ""
+    #set reference_database_name = "gg"
+  #else
+    #set reference_database_name = "silva"
+  #end if
+
+  ## Run the amplicon analysis pipeline wrapper
+  python $__tool_directory__/amplicon_analysis_pipeline.py
+  ## Set options
+  #if str( $forward_pcr_primer ) != ""
+  -g "$forward_pcr_primer"
+  #end if
+  #if str( $reverse_pcr_primer ) != ""
+  -G "$reverse_pcr_primer"
+  #end if
+  #if str( $trimming_threshold ) != ""
+  -q $trimming_threshold
+  #end if
+  #if str( $sliding_window_length ) != ""
+  -l $sliding_window_length
+  #end if
+  #if str( $minimum_overlap ) != ""
+  -O $minimum_overlap
+  #end if
+  #if str( $minimum_length ) != ""
+  -L $minimum_length
+  #end if
+  -P $pipeline
+  -r \$AMPLICON_ANALYSIS_REF_DATA_PATH
+  #if str( $reference_database ) != ""
+    "${reference_database}"
+  #end if
+  #if str($categories_file_in) != 'None'
+    -c "${categories_file_in}"
+  #end if
+  ## Input files
+  "${metatable_file_in}"
+  ## FASTQ pairs
+  #if str($input_type.pairs_or_collection) == "collection"
+    #set fastq_pairs = $input_type.fastq_collection
+  #else
+    #set fastq_pairs = $input_type.fastq_pairs
+  #end if
+  #for $fq_pair in $fastq_pairs
+    "${fq_pair.name}" "${fq_pair.forward}" "${fq_pair.reverse}"
+  #end for
+  &&
+
+  ## Collect outputs
+  cp Metatable_log/Metatable_mod.txt "${metatable_mod}" &&
+  cp ${pipeline}_OTU_tables/multiplexed_linearized_dereplicated_mc2_repset_nonchimeras_tax_OTU_table.biom "${tax_otu_table_biom_file}" &&
+  cp ${pipeline}_OTU_tables/otus.tre "${otus_tre_file}" &&
+  cp RESULTS/${pipeline}_${reference_database_name}/OTUs_count.txt "${otus_count_file}" &&
+  cp RESULTS/${pipeline}_${reference_database_name}/table_summary.txt "${table_summary_file}" &&
+  cp Multiplexed_files/${pipeline}_pipeline/multiplexed_linearized_dereplicated_mc2_repset_nonchimeras_OTUs.fasta "${dereplicated_nonchimera_otus_fasta}" &&
+  cp QUALITY_CONTROL/Reads_count.txt "$read_counts_out" &&
+  cp fastqc_quality_boxplots.html "${fastqc_quality_boxplots_html}" &&
+
+  ## HTML outputs
+
+  ## OTU table
+  mkdir $heatmap_otu_table_html.files_path &&
+  cp -r RESULTS/${pipeline}_${reference_database_name}/Heatmap/js $heatmap_otu_table_html.files_path &&
+  cp RESULTS/${pipeline}_${reference_database_name}/Heatmap/otu_table.html "${heatmap_otu_table_html}" &&
+
+  ## Phylum genus barcharts
+  mkdir $phylum_genus_dist_barcharts_html.files_path &&
+  cp -r RESULTS/${pipeline}_${reference_database_name}/phylum_genus_charts/charts $phylum_genus_dist_barcharts_html.files_path &&
+  cp -r RESULTS/${pipeline}_${reference_database_name}/phylum_genus_charts/raw_data $phylum_genus_dist_barcharts_html.files_path &&
+  cp RESULTS/${pipeline}_${reference_database_name}/phylum_genus_charts/bar_charts.html "${phylum_genus_dist_barcharts_html}" &&
+
+  ## Beta diversity weighted 2d plots
+  mkdir $beta_div_even_weighted_2d_plots.files_path &&
+  cp -r RESULTS/${pipeline}_${reference_database_name}/beta_div_even/weighted_2d_plot/* $beta_div_even_weighted_2d_plots.files_path &&
+  cp RESULTS/${pipeline}_${reference_database_name}/beta_div_even/weighted_2d_plot/weighted_unifrac_pc_2D_PCoA_plots.html "${beta_div_even_weighted_2d_plots}" &&
+
+  ## Beta diversity unweighted 2d plots
+  mkdir $beta_div_even_unweighted_2d_plots.files_path &&
+  cp -r RESULTS/${pipeline}_${reference_database_name}/beta_div_even/unweighted_2d_plot/* $beta_div_even_unweighted_2d_plots.files_path &&
+  cp RESULTS/${pipeline}_${reference_database_name}/beta_div_even/unweighted_2d_plot/unweighted_unifrac_pc_2D_PCoA_plots.html "${beta_div_even_unweighted_2d_plots}" &&
+
+  ## Alpha diversity rarefaction plots
+  mkdir $alpha_div_rarefaction_plots.files_path &&
+  cp RESULTS/${pipeline}_${reference_database_name}/Alpha_diversity/rarefaction_curves/rarefaction_plots.html $alpha_div_rarefaction_plots &&
+  cp -r RESULTS/${pipeline}_${reference_database_name}/Alpha_diversity/rarefaction_curves/average_plots $alpha_div_rarefaction_plots.files_path &&
+
+  ## Categories data
+  #if str($categories_file_in) != 'None'
+    ## Alpha diversity boxplots
+    mkdir $alpha_div_boxplots.files_path &&
+    cp alpha_diversity_boxplots.html "$alpha_div_boxplots" &&
+    cp RESULTS/${pipeline}_${reference_database_name}/Alpha_diversity/Alpha_diversity_boxplot/Categories_shannon/*.pdf $alpha_div_boxplots.files_path &&
+  #end if
+
+  ## Pipeline outputs (log files etc)
+  mkdir $log_files.files_path &&
+  cp Amplicon_analysis_pipeline.log $log_files.files_path &&
+  cp pipeline.log $log_files.files_path &&
+  cp Pipeline_outputs.txt $log_files.files_path &&
+  cp Metatable_log/Metatable.html $log_files.files_path &&
+  cp pipeline_outputs.html "$log_files"
+  ]]></command>
+  <inputs>
+    <param name="title" type="text" value="test" size="25"
+	   label="Title" help="Optional text that will be added to the output dataset names" />
+    <param type="data" name="metatable_file_in" format="tabular"
+	   label="Input Metatable.txt file" />
+    <param type="data" name="categories_file_in" format="txt"
+	   label="Input Categories.txt file" optional="true"
+	   help="(optional)" />
+    <conditional name="input_type">
+      <param name="pairs_or_collection" type="select"
+	     label="Input FASTQ type">
+	<option value="pairs_of_files">Pairs of datasets</option>
+	<option value="collection" selected="true">Dataset pairs in a collection</option>
+      </param>
+      <when value="collection">
+	<param name="fastq_collection" type="data_collection"
+	       format="fastqsanger,fastq" collection_type="list:paired"
+	       label="Collection of FASTQ forward and reverse (R1/R2) pairs"
+	       help="Each FASTQ pair will be treated as one sample; the name of each sample will be taken from the first column of the Metatable file " />
+      </when>
+      <when value="pairs_of_files">
+	<repeat name="fastq_pairs" title="Input fastq pairs" min="1">
+	  <param type="text" name="name" value=""
+		 label="Final name for FASTQ pair" />
+	  <param type="data" name="fastq_r1" format="fastqsanger,fastq"
+		 label="FASTQ with forward reads (R1)" />
+	  <param type="data" name="fastq_r2" format="fastqsanger,fastq"
+		 label="FASTQ with reverse reads (R2)" />
+	</repeat>
+      </when>
+    </conditional>
+    <param type="text" name="forward_pcr_primer" value=""
+	   label="Forward PCR primer sequence"
+	   help="Optional; must not include barcode or adapter sequence (-g)" />
+    <param type="text" name="reverse_pcr_primer" value=""
+	   label="Reverse PCR primer sequence"
+	   help="Optional; must not include barcode or adapter sequence (-G)" />
+    <param type="integer" name="trimming_threshold" value="20"
+	   label="Threshold quality below which read will be trimmed"
+	   help="Phred score; default is 20 (-q)" />
+    <param type="integer" name="minimum_overlap" value="10"
+	   label="Minimum overlap in bp between forward and reverse reads"
+	   help="Default is 10 (-O)" />
+    <param type="integer" name="minimum_length" value="200"
+	   label="Minimum length in bp to keep sequence after overlapping"
+	   help="Default is 200 (-L)" />
+    <param type="integer" name="sliding_window_length" value="10"
+	   label="Minimum length in bp to retain a read after trimming"
+	   help="Supplied to Sickle; default is 10 (-l)" />
+    <param type="select" name="pipeline"
+	    label="Pipeline to use for analysis">
+      <option value="Vsearch" selected="true" >Vsearch</option>
+      <!--
+      Remove the QIIME and Uparse options for now
+      <option value="QIIME">QIIME</option>
+      <option value="Uparse">Uparse</option>
+      -->
+    </param>
+    <param type="select" name="reference_database"
+	   label="Reference database">
+      <option value="" selected="true">GreenGenes</option>
+      <option value="-S">Silva</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="tabular" name="metatable_mod"
+	  label="${tool.name}:${title} Metatable_mod.txt" />
+    <data format="tabular" name="read_counts_out"
+	  label="${tool.name} (${pipeline}):${title} read counts" />
+    <data format="biom" name="tax_otu_table_biom_file"
+	  label="${tool.name} (${pipeline}):${title} tax OTU table (biom format)" />
+    <data format="tabular" name="otus_tre_file"
+	  label="${tool.name} (${pipeline}):${title} otus.tre" />
+    <data format="html" name="phylum_genus_dist_barcharts_html"
+	  label="${tool.name} (${pipeline}):${title} phylum genus dist barcharts HTML" />
+    <data format="tabular" name="otus_count_file"
+	  label="${tool.name} (${pipeline}):${title} OTUs count file" />
+    <data format="tabular" name="table_summary_file"
+	  label="${tool.name} (${pipeline}):${title} table summary file" />
+    <data format="fasta" name="dereplicated_nonchimera_otus_fasta"
+	  label="${tool.name} (${pipeline}):${title} multiplexed linearized dereplicated mc2 repset nonchimeras OTUs FASTA" />
+    <data format="html" name="fastqc_quality_boxplots_html"
+	  label="${tool.name} (${pipeline}):${title} FastQC per-base quality boxplots HTML" />
+    <data format="html" name="heatmap_otu_table_html"
+	  label="${tool.name} (${pipeline}):${title} heatmap OTU table HTML" />
+    <data format="html" name="beta_div_even_weighted_2d_plots"
+	  label="${tool.name} (${pipeline}):${title} beta diversity weighted 2D plots HTML" />
+    <data format="html" name="beta_div_even_unweighted_2d_plots"
+	  label="${tool.name} (${pipeline}):${title} beta diversity unweighted 2D plots HTML" />
+    <data format="html" name="alpha_div_rarefaction_plots"
+	  label="${tool.name} (${pipeline}):${title} alpha diversity rarefaction plots HTML" />
+    <data format="html" name="alpha_div_boxplots"
+	  label="${tool.name} (${pipeline}):${title} alpha diversity boxplots">
+      <filter>categories_file_in is not None</filter>
+    </data>
+    <data format="html" name="log_files"
+	  label="${tool.name} (${pipeline}):${title} log files" />
+  </outputs>
+  <tests>
+  </tests>
+  <help><![CDATA[
+
+What it does
+------------
+
+This pipeline has been designed for the analysis of 16S rRNA data from
+Illumina Miseq (Casava >= 1.8) paired-end reads.
+  
+Usage
+-----
+
+1. Preparation of the mapping file and format of unique sample id
+*****************************************************************
+
+Before using the amplicon analysis pipeline it would be necessary to
+follow the steps as below to avoid analysis failures and ensure samples
+are labelled appropriately. Sample names for the labelling are derived
+from the fastq files names that are generated from the sequencing. The
+labels will include everything between the beginning of the name and
+the sample number (from C11 to S19 in Fig. 1)
+
+.. image:: Pipeline_description_Fig1.png
+   :height: 46
+   :width: 382
+
+**Figure 1**
+
+If analysing 16S data from multiple runs: 
+
+The samples from different runs may have identical IDs. For example,
+when sequencing the same samples twice, by chance, these could be at
+the same position in both the runs. This would cause the fastq files
+to have exactly the same IDs (Fig. 2).
+
+.. image:: Pipeline_description_Fig2.png
+   :height: 100
+   :width: 463
+
+**Figure 2**
+
+In case of identical sample IDs the pipeline will fail to run and
+generate an error at the beginning of the analysis.
+
+To avoid having to change the file names, before uploading the files,
+ensure that the samples IDs are not repeated. 
+
+2. To upload the file
+*********************
+
+Click on **Get Data/Upload File** from the Galaxy tool panel on the
+left hand side.
+
+From the pop-up window, choose how to upload the file. The
+**Choose local file** option can be used for files up to 4Gb. Fastq files
+from Illumina MiSeq will rarely be bigger than 4Gb and this option is
+recommended.
+
+After choosing the files click **Start** to begin the upload. The window can
+now be closed and the files will be uploaded onto the Galaxy server. You
+will see the progress on the ``HISTORY`` panel on the right
+side of the screen. The colour will change from grey (queuing), to yellow
+(uploading) and finally green (uploaded).
+
+Once all the files are uploaded, click on the operations on multiple
+datasets icon and select the fastq files that need to be analysed.
+Click on the tab **For all selected...** and on the option
+**Build List of Dataset pairs** (Fig. 3).
+
+.. image:: Pipeline_description_Fig3.png
+   :height: 247
+   :width: 586
+
+**Figure 3**
+
+Change the filter parameter ``_1`` and ``_2`` to be ``_R1`` and ``_R2``.
+The fastq files forward R1 and reverse R2 should now appear in the
+corresponding columns.
+
+Select **Autopair**. This creates a collection of paired fastq files for
+the forward and reverse reads for each sample. The name of the pairs will
+be the ones used by the pipeline. You are free to change the names at this
+point as long as they are the same used in the Metatable file
+(see section 3).
+
+Name the collection and click on **create list**. This reduces the time
+required to input the forward and reverse reads for each individual sample.
+
+3. Create the Metatable files
+*****************************
+
+Metatable.txt
+~~~~~~~~~~~~~
+
+Click on the list of pairs you just created to see the name of the single
+pairs. The name of the pairs will be the ones used by the pipeline,
+therefore, these are the names that need to be used in the Metatable file.
+
+The Metatable file has to be in QIIME format. You can find a description
+of it on QIIME website http://qiime.org/documentation/file_formats.html
+
+EXAMPLE::
+
+    #SampleID    BarcodeSequence    LinkerPrimerSequence    Disease    Gender    Description
+    Mock-RUN1    TAAGGCGAGCGTAAGA                           PsA        Male      Control
+    Mock-RUN2    CGTACTAGGCGTAAGA                           PsA        Male      Control
+    Mock-RUN3    AGGCAGAAGCGTAAGA                           PsC        Female    Control
+
+Briefly: the column ``LinkerPrimerSequence`` is empty but it cannot be
+deleted. The header is very important. ``#SampleID``, ``Barcode``,
+``LinkerPrimerSequence`` and ``Description`` are mandatory. Between
+``LinkerPrimerSequence`` and ``Description`` you can add as many columns
+as you want. For every column a PCoA plot will be created (see
+**Results** section). You can create this file in Excel and it will have
+to be saved as ``Text(Tab delimited)``.
+
+During the analysis the Metatable.txt will be checked to ensure that the
+file has the correct format. If necessary, this will be modified and will
+be available as Metatable_corrected.txt in the history panel. If you are
+going to use the metatable file for any other statistical analyses,
+remember to use the ``Metatable_mod.txt`` one, otherwise the sample
+names might not match!
+
+Categories.txt (optional) 
+~~~~~~~~~~~~~~~~~~~~~~~~~
+
+This file is required if you want to get box plots for comparison of
+alpha diversity indices (see **Results** section). The file is a list
+(without header and IN ONE COLUMN) of categories present in the
+Metatable.txt file. THE NAMES YOU ARE USING HAVE TO BE THE SAME AS THE
+ONES USED IN THE METATABLE.TXT. You can create this file in Excel and
+will have to be saved as ``Text(Tab delimited)``.
+
+EXAMPLE::
+
+    Disease
+    Gender
+
+Metatable and categories files can be uploaded using Get Data as done
+with the fatsq files.
+
+4. Analysis
+***********
+
+Under **Amplicon_Analysis_Pipeline**
+
+ * **Title** Name to distinguish between the runs. It will be shown at
+   the beginning of each output file name.
+
+ * **Input Metatable.txt file** Select the Metatable.txt file related to
+   this analysis
+
+ * **Input Categories.txt file (Optional)** Select the Categories.txt file
+   related to this analysis
+
+ * **Input FASTQ type** select *Dataset pairs in a collection* and, then,
+   the collection of pairs you created earlier.
+
+ * **Forward/Reverse PCR primer sequence** if the PCR primer sequences
+   have not been removed from the MiSeq during the fastq creation, they
+   have to be removed before the analysis. Insert the PCR primer sequence
+   in the corresponding field. DO NOT include any barcode or adapter
+   sequence. If the PCR primers have been already trimmed by the MiSeq,
+   and you include the sequence in this field, this would lead to an error.
+   Only include the sequences if still present in the fastq files.
+
+ * **Threshold quality below which reads will be trimmed** Choose the
+   Phred score used by Sickle to trim the reads at the 3’ end.
+
+ * **Minimum length to retain a read after trimming** If the read length
+   after trimming is shorter than a user defined length, the read, along
+   with the corresponding read pair, will be discarded.
+
+ * **Minimum overlap in bp between forward and reverse reads** Choose the
+   minimum basepair overlap used by Pandaseq to assemble the reads.
+   Default is 10.
+
+ * **Minimum length in bp to keep a sequence after overlapping** Choose the
+   minimum sequence length used by Pandaseq to keep a sequence after the
+   overlapping. This depends on the expected amplicon length. Default is
+   380 (used for V3-V4 16S sequencing; expected length ~440bp)
+
+ * **Pipeline to use for analysis** Choose the pipeline to use for OTU
+   clustering and chimera removal. The Galaxy tool currently supports
+   ``Vsearch`` only. ``Uparse`` and ``QIIME`` are planned to be added
+   shortly (the tools are already available for the stand-alone pipeline).
+
+ * **Reference database** Choose between ``GreenGenes`` and ``Silva``
+   databases for taxa assignment.
+
+Click on **Execute** to start the analysis.
+
+5. Results
+**********
+
+Results are entirely generated using QIIME scripts. The results will 
+appear in the History panel when the analysis is completed
+
+ * **Vsearch_tax_OTU_table (biom format)** The OTU table in BIOM format
+   (http://biom-format.org/)
+
+ * **Vsearch_OTUs.tree** Phylogenetic tree constructed using
+   ``make_phylogeny.py`` (fasttree) QIIME script
+   (http://qiime.org/scripts/make_phylogeny.html)
+
+ * **Vsearch_phylum_genus_dist_barcharts_HTML** HTML file with bar
+   charts at Phylum, Genus and Species level
+   (http://qiime.org/scripts/summarize_taxa.html and
+   http://qiime.org/scripts/plot_taxa_summary.html)
+
+ * **Vsearch_OTUs_count_file** Summary of OTU counts per sample
+   (http://biom-format.org/documentation/summarizing_biom_tables.html)
+
+ * **Vsearch_table_summary_file** Summary of sequences counts per sample
+   (http://biom-format.org/documentation/summarizing_biom_tables.html)
+
+ * **Vsearch_multiplexed_linearized_dereplicated_mc2_repset_nonchimeras_OTUs.fasta**
+   Fasta file with OTU sequences
+
+ * **Vsearch_heatmap_OTU_table_HTML** Interactive OTU heatmap
+   (http://qiime.org/1.8.0/scripts/make_otu_heatmap_html.html )
+
+ * **Vsearch_beta_diversity_weighted_2D_plots_HTML** PCoA plots in HTML
+   format using weighted Unifrac distance measure. Samples are grouped
+   by the column names present in the Metatable file. The samples are
+   firstly rarefied to the minimum sequencing depth
+   (http://qiime.org/scripts/beta_diversity_through_plots.html )
+
+ * **Vsearch_beta_diversity_unweighted_2D_plots_HTML** PCoA plots in HTML
+   format using Unweighted Unifrac distance measure. Samples are grouped
+   by the column names present in the Metatable file. The samples are
+   firstly rarefied to the minimum sequencing depth
+   (http://qiime.org/scripts/beta_diversity_through_plots.html )
+
+Code availability
+-----------------
+
+**Code is available at** https://github.com/MTutino/Amplicon_analysis
+
+Credits
+-------
+
+Pipeline author: Mauro Tutino
+
+Galaxy tool: Peter Briggs
+
+	]]></help>
+  <citations>
+    <citation type="bibtex">
+      @misc{githubAmplicon_analysis,
+      author = {Tutino, Mauro},
+      year = {2017},
+      title = {Amplicon Analysis Pipeline},
+      publisher = {GitHub},
+      journal = {GitHub repository},
+      url = {https://github.com/MTutino/Amplicon_analysis},
+}</citation>
+  </citations>
+</tool>
diff -r 000000000000 -r 47ec9c6f44b8 install_tool_deps.sh
--- /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
+##
+#
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