Mercurial > repos > peterjc > tmhmm_and_signalp
comparison tools/protein_analysis/README @ 0:bca9bc7fdaef
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
| author | peterjc |
|---|---|
| date | Tue, 07 Jun 2011 18:03:34 -0400 |
| parents | |
| children | 3ff1dcbb9440 |
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| -1:000000000000 | 0:bca9bc7fdaef |
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| 1 This package contains Galaxy wrappers for two standalone command line protein | |
| 2 analysis tools (SignalP 3.0 and THMHMM 2.0) from the Center for Biological | |
| 3 Sequence Analysis at the Technical University of Denmark, | |
| 4 http://www.cbs.dtu.dk/cbs/ | |
| 5 | |
| 6 To use these Galaxy wrappers you must first install the CBS command line | |
| 7 tools. At the time of writing both SignalP 3.0 and TMHMM 2.0 are free for | |
| 8 academic use. | |
| 9 | |
| 10 These wrappers are copyright 2010 by Peter Cock, SCRI, UK. All rights | |
| 11 reserved. See the included LICENCE file for details. | |
| 12 | |
| 13 Installation | |
| 14 ============ | |
| 15 | |
| 16 1. Install the command line version of SignalP 3.0 and ensure it is on the | |
| 17 PATH, see: http://www.cbs.dtu.dk/services/SignalP/ | |
| 18 | |
| 19 2. Install the command line version of TMHMM 2.0 and ensure it is on the | |
| 20 PATH, see: http://www.cbs.dtu.dk/services/TMHMM/ | |
| 21 | |
| 22 3. Create a folder tools/protein_analysis under your Galaxy installation. | |
| 23 | |
| 24 4. Copy/move the following files (from this archive) there: | |
| 25 | |
| 26 tmhmm2.xml (Galaxy tool definition) | |
| 27 tmhmm2.py (Python wrapper script) | |
| 28 signalp3.xml (Galaxy tool definition) | |
| 29 signalp3.py (Python wrapper script) | |
| 30 seq_analysis_utils.py (shared Python code) | |
| 31 README (optional) | |
| 32 | |
| 33 5. Edit your Galaxy conjuration file tool_conf.xml (to use the tools) AND | |
| 34 also tool_conf.xml.sample (to run the tests) to include the two new tools | |
| 35 by adding: | |
| 36 | |
| 37 <section name="Protein sequence analysis" id="protein_analysis"> | |
| 38 <tool file="protein_analysis/tmhmm2.xml" /> | |
| 39 <tool file="protein_analysis/signalp3.xml" /> | |
| 40 </section> | |
| 41 | |
| 42 6. Copy/move the following test files (from these archive) to Galaxy | |
| 43 subfolder test-data: | |
| 44 | |
| 45 four_human_proteins.fasta | |
| 46 four_human_proteins.signalp3.tsv | |
| 47 four_human_proteins.tmhmm2.tsv | |
| 48 | |
| 49 7. Run the Galaxy functional tests for these new wrappers with: | |
| 50 | |
| 51 ./run_functional_tests.sh -id tmhmm2 | |
| 52 ./run_functional_tests.sh -id signalp3 | |
| 53 | |
| 54 Alternatively, this should work (assuming you left the name and id as shown in | |
| 55 the XML file tool_conf.xml.sample): | |
| 56 | |
| 57 ./run_functional_tests.sh -sid Protein_sequence_analysis-protein_analysis | |
| 58 | |
| 59 8. Restart Galaxy and check the new tools are shown and work. |