Mercurial > repos > peterjc > tmhmm_and_signalp

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+++ b/tools/protein_analysis/README.rst	Tue Sep 17 12:06:15 2013 -0400
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+This package contains Galaxy wrappers for a selection of standalone command
+line protein analysis tools:
+
+* SignalP 3.0, THMHMM 2.0, Promoter 2.0 from the Center for Biological
+  Sequence Analysis at the Technical University of Denmark,
+  http://www.cbs.dtu.dk/cbs/
+
+* WoLF PSORT v0.2 from http://wolfpsort.org/
+
+* PSORTb v3 from http://www.psort.org/downloads/index.html
+
+Also, the RXLR motif tool uses SignalP 3.0 and HMMER 2.3.2 internally.
+
+To use these Galaxy wrappers you must first install the command line tools.
+At the time of writing they are all free for academic use, or open source.
+
+These wrappers are copyright 2010-2013 by Peter Cock, James Hutton Institute
+(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
+Contributions/revisions copyright 2011 Konrad Paszkiewicz. All rights reserved.
+See the included LICENCE file for details (MIT open source licence).
+
+The wrappers are available from the Galaxy Tool Shed
+http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
+
+Citation
+========
+
+If you use any of these Galaxy tools in work leading to a scientific
+publication, in addition to citing the invididual underlying tools, please cite:
+
+Peter Cock, Bjoern Gruening, Konrad Paszkiewicz and Leighton Pritchard (2013).
+Galaxy tools and workflows for sequence analysis with applications
+in molecular plant pathology. PeerJ 1:e167
+http://dx.doi.org/10.7717/peerj.167
+
+Full reference information is included in the help text for each tool.
+
+
+Requirements
+============
+
+First install those command line tools you wish to use the wrappers for:
+
+1. Install the command line version of SignalP 3.0 and ensure "signalp" is
+   on the PATH, see: http://www.cbs.dtu.dk/services/SignalP/
+
+2. Install the command line version of TMHMM 2.0 and ensure "tmhmm" is on
+   the PATH, see: http://www.cbs.dtu.dk/services/TMHMM/
+
+3. Install the command line version of Promoter 2.0 and ensure "promoter" is
+   on the PATH, see: http://www.cbs.dtu.dk/services/Promoter
+
+4. Install the WoLF PSORT v0.2 package, and ensure "runWolfPsortSummary"
+   is on the PATH (we use an extra wrapper script to change to the WoLF PSORT
+   directory, run runWolfPsortSummary, and then change back to the original
+   directory), see: http://wolfpsort.org/WoLFPSORT_package/version0.2/
+
+5. Install hmmsearch from HMMER 2.3.2 (the last stable release of HMMER 2)
+   but put it on the path under the name hmmsearch2 (allowing it to co-exist
+   with HMMER 3), or edit rlxr_motif.py accordingly.
+
+Verify each of the tools is installed and working from the command line
+(when logged in as the Galaxy user if appropriate).
+
+
+Manual Installation
+===================
+
+1. Create a folder tools/protein_analysis under your Galaxy installation.
+   This folder name is not critical, and can be changed if desired - you
+   must update the paths used in tool_conf.xml to match.
+
+2. Copy/move the following files (from this archive) there:
+
+   * tmhmm2.xml (Galaxy tool definition)
+   * tmhmm2.py (Python wrapper script)
+
+   * signalp3.xml (Galaxy tool definition)
+   * signalp3.py (Python wrapper script)
+
+   * promoter2.xml (Galaxy tool definition)
+   * promoter2.py (Python wrapper script)
+
+   * psortb.xml (Galaxy tool definition)
+   * psortb.py (Python wrapper script)
+
+   * wolf_psort.xml (Galaxy tool definition)
+   * wolf_psort.py (Python wrapper script)
+
+   * rxlr_motifs.xml (Galaxy tool definition)
+   * rxlr_motifs.py (Python script)
+
+   * seq_analysis_utils.py (shared Python code)
+   * LICENCE
+   * README.rst (this file)
+
+3. Edit your Galaxy conjuration file tool_conf.xml (to use the tools) AND
+   also tool_conf.xml.sample (to run the tests) to include the new tools
+   by adding::
+
+    <section name="Protein sequence analysis" id="protein_analysis">
+      <tool file="protein_analysis/tmhmm2.xml" />
+      <tool file="protein_analysis/signalp3.xml" />
+      <tool file="protein_analysis/psortb.xml" />
+      <tool file="protein_analysis/wolf_psort.xml" />
+      <tool file="protein_analysis/rxlr_motifs.xml" />
+    </section>
+    <section name="Nucleotide sequence analysis" id="nucleotide_analysis">
+      <tool file="protein_analysis/promoter2.xml" />
+    </section>
+
+   Leave out the lines for any tools you do not wish to use in Galaxy.
+
+4. Copy/move the test-data files (from this archive) to Galaxy's
+   subfolder test-data.
+
+5. Run the Galaxy functional tests for these new wrappers with::
+
+    ./run_functional_tests.sh -id tmhmm2
+    ./run_functional_tests.sh -id signalp3
+    ./run_functional_tests.sh -id Psortb
+    ./run_functional_tests.sh -id rxlr_motifs
+
+   Alternatively, this should work (assuming you left the name and id as shown in
+   the XML file tool_conf.xml.sample)::
+
+    ./run_functional_tests.sh -sid Protein_sequence_analysis-protein_analysis
+
+   To check the section ID expected, use ./run_functional_tests.sh -list
+
+6. Restart Galaxy and check the new tools are shown and work.
+
+
+History
+=======
+
+======= ======================================================================
+Version Changes
+------- ----------------------------------------------------------------------
+v0.0.1  - Initial release
+v0.0.2  - Corrected some typos in the help text
+        - Renamed test output file to use Galaxy convention of *.tabular
+v0.0.3  - Check for tmhmm2 silent failures (no output)
+        - Additional unit tests
+v0.0.4  - Ignore comment lines in tmhmm2 output.
+v0.0.5  - Explicitly request tmhmm short output (may not be the default)
+v0.0.6  - Improvement to how sub-jobs are run (should be faster)
+v0.0.7  - Change SignalP default truncation from 60 to 70 to match the
+          SignalP webservice.
+v0.0.8  - Added WoLF PSORT wrapper to the suite.
+v0.0.9  - Added our RXLR motifs tool to the suite.
+v0.1.0  - Added Promoter 2.0 wrapper (similar to SignalP & TMHMM wrappers)
+        - Support Galaxy's <parallelism> tag for SignalP, TMHMM & Promoter
+v0.1.1  - Fixed an error in the header of the tabular output from Promoter
+v0.1.2  - Use the new <stdio> settings in the XML wrappers to catch errors
+        - Use SGE style $NSLOTS for thread count (otherwise default to 4)
+v0.1.3  - Added missing file whisson_et_al_rxlr_eer_cropped.hmm to Tool Shed
+v0.2.0  - Added PSORTb wrapper to the suite, based on earlier work
+          contributed by Konrad Paszkiewicz.
+v0.2.1  - Use a script to create the Tool Shed tar-ball (removed some stray
+          files accidentally included previously via a wildcard).
+v0.2.2  - Include missing test files.
+v0.2.3  - Added unit tests for WoLF PSORT.
+v0.2.4  - Added unit tests for Promoter 2
+v0.2.5  - Link to Tool Shed added to help text and this documentation.
+        - More unit tests.
+        - Fixed bug with RXLR tool and empty FASTA files.
+        - Fixed typo in the RXLR tool help text.
+        - Updated citation information (Cock et al. 2013).
+        - Adopted standard MIT licence.
+        - Use reStructuredText for this README file.
+        - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
+======= ======================================================================
+
+
+Developers
+==========
+
+This script and other tools are being developed on the following hg branches:
+http://bitbucket.org/peterjc/galaxy-central/src/seq_analysis
+http://bitbucket.org/peterjc/galaxy-central/src/tools
+
+Development has now moved to a dedicated GitHub repository:
+https://github.com/peterjc/pico_galaxy/tree/master/tools
+
+For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use
+the following command from the Galaxy root folder::
+
+    $ ./tools/protein_analysis/make_tmhmm_and_signalp.sh
+
+This simplifies ensuring a consistent set of files is bundled each time,
+including all the relevant test files.