Mercurial > repos > peterjc > tmhmm_and_signalp
changeset 23:1f7678c1f4ad draft
Uploaded v0.2.5 take 7, using RST for README file; development moved to GitHub
| author | peterjc |
|---|---|
| date | Tue, 17 Sep 2013 12:05:12 -0400 |
| parents | 90e3d02f8013 |
| children | ee10017fcd80 |
| files | tools/protein_analysis/README.txt |
| diffstat | 1 files changed, 0 insertions(+), 185 deletions(-) [+] |
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--- a/tools/protein_analysis/README.txt Thu Sep 12 11:06:04 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,185 +0,0 @@ -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 (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 -======= - -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 $NSLOTS for thread count (otherwise default to 4) -v0.1.3 - Added missing file whisson_et_al_rxlr_eer_cropped.hmm to Tool Shed -v0.2.0 - Added PSORTb wrapper to the suite, based on earlier work - contributed by Konrad Paszkiewicz. -v0.2.1 - Use a script to create the Tool Shed tar-ball (removed some stray - files accidentally included previously via a wildcard). -v0.2.2 - Include missing test files. -v0.2.3 - Added unit tests for WoLF PSORT. -v0.2.4 - Added unit tests for Promoter 2 -v0.2.5 - Link to Tool Shed added to help text and this documentation. - - More unit tests. - - Fixed bug with RXLR tool and empty FASTA files. - - Fixed typo in the RXLR tool help text. - - Updated citation information (Cock et al. 2013). - - Adopted standard MIT licence. - - -Developers -========== - -This script and other tools are being developed on the following hg branch: -http://bitbucket.org/peterjc/galaxy-central/src/tools - -This incorporates the previously used hg branch: -http://bitbucket.org/peterjc/galaxy-central/src/seq_analysis - -For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use -the following command from the Galaxy root folder: - -$ ./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.