Mercurial > repos > pjbriggs > amplicon_analysis_pipeline

--- a/README	Mon Jun 18 07:54:54 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,252 +0,0 @@
-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
- - spades 3.5.0
- - qiime 1.8.0
- - blast-legacy 2.2.26
- - vsearch 1.1.3
- - fasta-splitter 0.2.4
- - rdp_classifier 2.2
-
-The following dependencies are currently unavailable:
-
- - fasta_number (need 02jun2015)
- - 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
----------- ----------------------------------------------------------------------
-1.2.2.1    Update to get dependencies from bioconda
-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
-           option to use the Human Oral Microbiome Database v15.1, and
-           updates SILVA database to v123)
-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
-========== ======================================================================
--- a/amplicon_analysis_pipeline.py	Mon Jun 18 07:54:54 2018 -0400
+++ b/amplicon_analysis_pipeline.py	Mon Jun 18 10:05:58 2018 -0400
@@ -191,6 +191,7 @@
             find_executable("fasta-splitter"))
     if fasta_splitter:
         os.symlink(vsearch,os.path.join("bin","fasta-splitter.pl"))
+        print "-- made symlink to %s" % fasta_splitter
     else:
         sys.stderr.write("Missing 'fasta-splitter[.pl]'\n")
--- a/tool_dependencies.xml	Mon Jun 18 07:54:54 2018 -0400
+++ b/tool_dependencies.xml	Mon Jun 18 10:05:58 2018 -0400
@@ -24,6 +24,10 @@
 	    <source>THIRD_STEP.sh</source>
 	    <destination>$INSTALL_DIR/Amplicon_analysis_pipeline</destination>
 	  </action>
+	  <action type="move_directory_files">
+	    <source>uc2otutab</source>
+	    <destination>$INSTALL_DIR/Amplicon_analysis_pipeline/uc2otutab</destination>
+	  </action>
 	  <action type="set_environment">
 	    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/Amplicon_analysis_pipeline</environment_variable>
 	  </action>