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comparison tools/protein_analysis/README @ 6:a290c6d4e658

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Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
author peterjc
date Tue, 07 Jun 2011 18:07:09 -0400
parents 0f1c61998b22
children 9b45a8743100
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5:0f1c61998b22 6:a290c6d4e658
4 * SignalP 3.0 and THMHMM 2.0, from the Center for Biological 4 * SignalP 3.0 and THMHMM 2.0, from the Center for Biological
5 Sequence Analysis at the Technical University of Denmark, 5 Sequence Analysis at the Technical University of Denmark,
6 http://www.cbs.dtu.dk/cbs/ 6 http://www.cbs.dtu.dk/cbs/
7 7
8 * WoLF PSORT v0.2 from http://wolfpsort.org/ 8 * WoLF PSORT v0.2 from http://wolfpsort.org/
9
10 Also, the RXLR motif tool uses SignalP 3.0 and HMMER 2.3.2 internally.
9 11
10 To use these Galaxy wrappers you must first install the command line tools. 12 To use these Galaxy wrappers you must first install the command line tools.
11 At the time of writing they are all free for academic use. 13 At the time of writing they are all free for academic use.
12 14
13 These wrappers are copyright 2010-2011 by Peter Cock, James Hutton Institute 15 These wrappers are copyright 2010-2011 by Peter Cock, James Hutton Institute
28 3. Install the WoLF PSORT v0.2 package, and ensure "runWolfPsortSummary" 30 3. Install the WoLF PSORT v0.2 package, and ensure "runWolfPsortSummary"
29 is on the PATH (we use an extra wrapper script to change to the WoLF PSORT 31 is on the PATH (we use an extra wrapper script to change to the WoLF PSORT
30 directory, run runWolfPsortSummary, and then change back to the original 32 directory, run runWolfPsortSummary, and then change back to the original
31 directory), see: http://wolfpsort.org/WoLFPSORT_package/version0.2/ 33 directory), see: http://wolfpsort.org/WoLFPSORT_package/version0.2/
32 34
35 4. Install hmmsearch from HMMER 2.3.2 (the last stable release of HMMER 2)
36 but put it on the path under the name hmmsearch2 (allowing it to co-exist
37 with HMMER 3), or edit rlxr_motif.py accordingly.
38
33 Verify each of the tools is installed and working from the command line 39 Verify each of the tools is installed and working from the command line
34 (when logged in at the Galaxy user if appropriate). 40 (when logged in at the Galaxy user if appropriate).
35 41
36 Installation 42 Installation
37 ============ 43 ============
47 signalp3.py (Python wrapper script) 53 signalp3.py (Python wrapper script)
48 54
49 wolf_psort.xml (Galaxy tool definition) 55 wolf_psort.xml (Galaxy tool definition)
50 wolf_psort.py (Python wrapper script) 56 wolf_psort.py (Python wrapper script)
51 57
58 rxlr_motifs.xml (Galaxy tool definition)
59 rxlr_motifs.py (Python script)
60
52 seq_analysis_utils.py (shared Python code) 61 seq_analysis_utils.py (shared Python code)
53 README (optional) 62 README (optional)
54 63
55 3. Edit your Galaxy conjuration file tool_conf.xml (to use the tools) AND 64 3. Edit your Galaxy conjuration file tool_conf.xml (to use the tools) AND
56 also tool_conf.xml.sample (to run the tests) to include the new tools 65 also tool_conf.xml.sample (to run the tests) to include the new tools
58 67
59 <section name="Protein sequence analysis" id="protein_analysis"> 68 <section name="Protein sequence analysis" id="protein_analysis">
60 <tool file="protein_analysis/tmhmm2.xml" /> 69 <tool file="protein_analysis/tmhmm2.xml" />
61 <tool file="protein_analysis/signalp3.xml" /> 70 <tool file="protein_analysis/signalp3.xml" />
62 <tool file="protein_analysis/wolf_psort.xml" /> 71 <tool file="protein_analysis/wolf_psort.xml" />
72 <tool file="protein_analysis/rxlr_motifs.xml" />
63 </section> 73 </section>
64 74
65 Leave out the lines for any tools you do not wish to use in Galaxy. 75 Leave out the lines for any tools you do not wish to use in Galaxy.
66 76
67 4. Copy/move the following test files (from these archive) to Galaxy 77 4. Copy/move the following test files (from these archive) to Galaxy
99 v0.0.5 - Explicitly request tmhmm short output (may not be the default) 109 v0.0.5 - Explicitly request tmhmm short output (may not be the default)
100 v0.0.6 - Improvement to how sub-jobs are run (should be faster) 110 v0.0.6 - Improvement to how sub-jobs are run (should be faster)
101 v0.0.7 - Change SignalP default truncation from 60 to 70 to match the 111 v0.0.7 - Change SignalP default truncation from 60 to 70 to match the
102 SignalP webservice. 112 SignalP webservice.
103 v0.0.8 - Added WoLF PSORT wrapper to the suite. 113 v0.0.8 - Added WoLF PSORT wrapper to the suite.
114 v0.0.9 - Added our RXLR motifs tool to the suite.
104 115
105 116
106 Developers 117 Developers
107 ========== 118 ==========
108 119
113 http://bitbucket.org/peterjc/galaxy-central/src/seq_analysis 124 http://bitbucket.org/peterjc/galaxy-central/src/seq_analysis
114 125
115 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use 126 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use
116 the following command from the Galaxy root folder: 127 the following command from the Galaxy root folder:
117 128
118 tar -czf tmhmm_signalp_wolfpsort.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/wolf_psort.xml tools/protein_analysis/wolf_psort.py test-data/four_human_proteins.* test-data/empty.fasta test-data/empty_tmhmm2.tabular test-data/empty_signalp3.tabular 129 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/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
119 130
120 Check this worked: 131 Check this worked:
121 132
122 $ tar -tzf tmhmm_signalp_wolfpsort.tar.gz 133 $ tar -tzf tmhmm_signalp_etc.tar.gz
123 tools/protein_analysis/LICENSE 134 tools/protein_analysis/LICENSE
124 tools/protein_analysis/README 135 tools/protein_analysis/README
125 tools/protein_analysis/suite_config.xml 136 tools/protein_analysis/suite_config.xml
126 tools/protein_analysis/seq_analysis_utils.py 137 tools/protein_analysis/seq_analysis_utils.py
127 tools/protein_analysis/signalp3.xml 138 tools/protein_analysis/signalp3.xml
128 tools/protein_analysis/signalp3.py 139 tools/protein_analysis/signalp3.py
129 tools/protein_analysis/tmhmm2.xml 140 tools/protein_analysis/tmhmm2.xml
130 tools/protein_analysis/tmhmm2.py 141 tools/protein_analysis/tmhmm2.py
131 tools/protein_analysis/wolf_psort.xml 142 tools/protein_analysis/wolf_psort.xml
132 tools/protein_analysis/wolf_psort.py 143 tools/protein_analysis/wolf_psort.py
144 tools/protein_analysis/rxlr_motifs.xml
145 tools/protein_analysis/rxrl_motifs.py
133 test-data/four_human_proteins.fasta 146 test-data/four_human_proteins.fasta
134 test-data/four_human_proteins.signalp3.tabular 147 test-data/four_human_proteins.signalp3.tabular
135 test-data/four_human_proteins.tmhmm2.tabular 148 test-data/four_human_proteins.tmhmm2.tabular
136 test-data/empty.fasta 149 test-data/empty.fasta
137 test-data/empty_tmhmm2.tabular 150 test-data/empty_tmhmm2.tabular