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/ 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. These wrappers are copyright 2010-2012 by Peter Cock, James Hutton Institute (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. See the included LICENCE file for details (an MIT style open source licence). 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) 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:
Leave out the lines for any tools you do not wish to use in Galaxy. 4. Copy/move the following test files (from these archive) to Galaxy subfolder test-data: four_human_proteins.fasta four_human_proteins_signalp3.tabular four_human_proteins_tmhmm2.tabular empty.fasta empty_tmhmm2.tabular empty_signalp3.tabular 5. Run the Galaxy functional tests for these new wrappers with: ./run_functional_tests.sh -id tmhmm2 ./run_functional_tests.sh -id signalp3 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 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 tag for SignalP, TMHMM & Promoter v0.1.1 - Fixed an error in the header of the tabular output from Promoter 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: tar -czf ~/tmhmm_signalp_etc.tar.gz tools/protein_analysis/LICENSE tools/protein_analysis/README tools/protein_analysis/suite_config.xml tools/protein_analysis/seq_analysis_utils.py tools/protein_analysis/signalp3.xml tools/protein_analysis/signalp3.py tools/protein_analysis/tmhmm2.xml tools/protein_analysis/tmhmm2.py tools/protein_analysis/promoter2.xml tools/protein_analysis/promoter2.py tools/protein_analysis/wolf_psort.xml tools/protein_analysis/wolf_psort.py tools/protein_analysis/rxlr_motifs.xml tools/protein_analysis/rxlr_motifs.py test-data/four_human_proteins.* test-data/empty.fasta test-data/empty_tmhmm2.tabular test-data/empty_signalp3.tabular Check this worked: $ tar -tzf tmhmm_signalp_etc.tar.gz tools/protein_analysis/LICENSE tools/protein_analysis/README tools/protein_analysis/suite_config.xml tools/protein_analysis/seq_analysis_utils.py tools/protein_analysis/signalp3.xml tools/protein_analysis/signalp3.py tools/protein_analysis/tmhmm2.xml tools/protein_analysis/tmhmm2.py tools/protein_analysis/promoter2.xml tools/protein_analysis/promoter2.py tools/protein_analysis/wolf_psort.xml tools/protein_analysis/wolf_psort.py tools/protein_analysis/rxlr_motifs.xml tools/protein_analysis/rxrl_motifs.py test-data/four_human_proteins.fasta test-data/four_human_proteins.signalp3.tabular test-data/four_human_proteins.tmhmm2.tabular test-data/empty.fasta test-data/empty_tmhmm2.tabular test-data/empty_signalp3.tabular