# HG changeset patch # User peterjc # Date 1379433975 14400 # Node ID ee10017fcd80cd138c2ba225887a21b54a34930b # Parent 1f7678c1f4adc3c2235fdc0603a0948f5910c315 Uploaded v0.2.5 preview 8, omitted README.rst in last upload diff -r 1f7678c1f4ad -r ee10017fcd80 tools/protein_analysis/README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/protein_analysis/README.rst Tue Sep 17 12:06:15 2013 -0400 @@ -0,0 +1,192 @@ +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:: + +
+ + + + + +
+
+ +
+ + 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 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 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.