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comparison tools/protein_analysis/README @ 7:5e62aefb2918 draft

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Uploaded v0.1.2 to Test Tool Shed
author peterjc
date Tue, 26 Mar 2013 14:24:56 -0400
parents 39a6e46cdda3
children 391a142c1e60
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6:39a6e46cdda3 7:5e62aefb2918
1 This package contains Galaxy wrappers for a selection of standalone command 1 This package contains Galaxy wrappers for a selection of standalone command
2 line protein analysis tools: 2 line protein analysis tools:
3 3
4 * SignalP 3.0 and THMHMM 2.0, from the Center for Biological 4 * SignalP 3.0, THMHMM 2.0, Promoter 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 9
10 Also, the RXLR motif tool uses SignalP 3.0 and HMMER 2.3.2 internally. 10 Also, the RXLR motif tool uses SignalP 3.0 and HMMER 2.3.2 internally.
11 11
12 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.
13 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.
14 14
15 These wrappers are copyright 2010-2011 by Peter Cock, James Hutton Institute 15 These wrappers are copyright 2010-2012 by Peter Cock, James Hutton Institute
16 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. 16 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
17 See the included LICENCE file for details. 17 See the included LICENCE file for details (an MIT style open source licence).
18 18
19 Requirements 19 Requirements
20 ============ 20 ============
21 21
22 First install those command line tools you wish to use the wrappers for: 22 First install those command line tools you wish to use the wrappers for:
25 on the PATH, see: http://www.cbs.dtu.dk/services/SignalP/ 25 on the PATH, see: http://www.cbs.dtu.dk/services/SignalP/
26 26
27 2. Install the command line version of TMHMM 2.0 and ensure "tmhmm" is on 27 2. Install the command line version of TMHMM 2.0 and ensure "tmhmm" is on
28 the PATH, see: http://www.cbs.dtu.dk/services/TMHMM/ 28 the PATH, see: http://www.cbs.dtu.dk/services/TMHMM/
29 29
30 3. Install the WoLF PSORT v0.2 package, and ensure "runWolfPsortSummary" 30 3. Install the command line version of Promoter 2.0 and ensure "promoter" is
31 on the PATH, see: http://www.cbs.dtu.dk/services/Promoter
32
33 4. Install the WoLF PSORT v0.2 package, and ensure "runWolfPsortSummary"
31 is on the PATH (we use an extra wrapper script to change to the WoLF PSORT 34 is on the PATH (we use an extra wrapper script to change to the WoLF PSORT
32 directory, run runWolfPsortSummary, and then change back to the original 35 directory, run runWolfPsortSummary, and then change back to the original
33 directory), see: http://wolfpsort.org/WoLFPSORT_package/version0.2/ 36 directory), see: http://wolfpsort.org/WoLFPSORT_package/version0.2/
34 37
35 4. Install hmmsearch from HMMER 2.3.2 (the last stable release of HMMER 2) 38 5. 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 39 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. 40 with HMMER 3), or edit rlxr_motif.py accordingly.
38 41
39 Verify each of the tools is installed and working from the command line 42 Verify each of the tools is installed and working from the command line
40 (when logged in at the Galaxy user if appropriate). 43 (when logged in as the Galaxy user if appropriate).
41 44
42 Installation 45 Manual Installation
43 ============ 46 ===================
44 47
45 1. Create a folder tools/protein_analysis under your Galaxy installation. 48 1. Create a folder tools/protein_analysis under your Galaxy installation.
49 This folder name is not critical, and can be changed if desired - you
50 must update the paths used in tool_conf.xml to match.
46 51
47 2. Copy/move the following files (from this archive) there: 52 2. Copy/move the following files (from this archive) there:
48 53
49 tmhmm2.xml (Galaxy tool definition) 54 tmhmm2.xml (Galaxy tool definition)
50 tmhmm2.py (Python wrapper script) 55 tmhmm2.py (Python wrapper script)
51 56
52 signalp3.xml (Galaxy tool definition) 57 signalp3.xml (Galaxy tool definition)
53 signalp3.py (Python wrapper script) 58 signalp3.py (Python wrapper script)
54 59
60 promoter2.xml (Galaxy tool definition)
61 promoter2.py (Python wrapper script)
62
55 wolf_psort.xml (Galaxy tool definition) 63 wolf_psort.xml (Galaxy tool definition)
56 wolf_psort.py (Python wrapper script) 64 wolf_psort.py (Python wrapper script)
57 65
58 rxlr_motifs.xml (Galaxy tool definition) 66 rxlr_motifs.xml (Galaxy tool definition)
59 rxlr_motifs.py (Python script) 67 rxlr_motifs.py (Python script)
60 68
61 seq_analysis_utils.py (shared Python code) 69 seq_analysis_utils.py (shared Python code)
62 README (optional) 70 LICENCE
71 README (this file)
63 72
64 3. Edit your Galaxy conjuration file tool_conf.xml (to use the tools) AND 73 3. Edit your Galaxy conjuration file tool_conf.xml (to use the tools) AND
65 also tool_conf.xml.sample (to run the tests) to include the new tools 74 also tool_conf.xml.sample (to run the tests) to include the new tools
66 by adding: 75 by adding:
67 76
68 <section name="Protein sequence analysis" id="protein_analysis"> 77 <section name="Protein sequence analysis" id="protein_analysis">
69 <tool file="protein_analysis/tmhmm2.xml" /> 78 <tool file="protein_analysis/tmhmm2.xml" />
70 <tool file="protein_analysis/signalp3.xml" /> 79 <tool file="protein_analysis/signalp3.xml" />
71 <tool file="protein_analysis/wolf_psort.xml" /> 80 <tool file="protein_analysis/wolf_psort.xml" />
72 <tool file="protein_analysis/rxlr_motifs.xml" /> 81 <tool file="protein_analysis/rxlr_motifs.xml" />
82 </section>
83 <section name="Nucleotide sequence analysis" id="nucleotide_analysis">
84 <tool file="protein_analysis/promoter2.xml" />
73 </section> 85 </section>
74 86
75 Leave out the lines for any tools you do not wish to use in Galaxy. 87 Leave out the lines for any tools you do not wish to use in Galaxy.
76 88
77 4. Copy/move the following test files (from these archive) to Galaxy 89 4. Copy/move the following test files (from these archive) to Galaxy
110 v0.0.6 - Improvement to how sub-jobs are run (should be faster) 122 v0.0.6 - Improvement to how sub-jobs are run (should be faster)
111 v0.0.7 - Change SignalP default truncation from 60 to 70 to match the 123 v0.0.7 - Change SignalP default truncation from 60 to 70 to match the
112 SignalP webservice. 124 SignalP webservice.
113 v0.0.8 - Added WoLF PSORT wrapper to the suite. 125 v0.0.8 - Added WoLF PSORT wrapper to the suite.
114 v0.0.9 - Added our RXLR motifs tool to the suite. 126 v0.0.9 - Added our RXLR motifs tool to the suite.
127 v0.1.0 - Added Promoter 2.0 wrapper (similar to SignalP & TMHMM wrappers)
128 - Support Galaxy's <parallelism> tag for SignalP, TMHMM & Promoter
129 v0.1.1 - Fixed an error in the header of the tabular output from Promoter
130 v0.1.2 - Use the new <stdio> settings in the XML wrappers to catch errors
131 - Use SGE style $NSLOTS for thread count (otherwise default to 4)
115 132
116 133
117 Developers 134 Developers
118 ========== 135 ==========
119 136
124 http://bitbucket.org/peterjc/galaxy-central/src/seq_analysis 141 http://bitbucket.org/peterjc/galaxy-central/src/seq_analysis
125 142
126 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use 143 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use
127 the following command from the Galaxy root folder: 144 the following command from the Galaxy root folder:
128 145
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 146 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
130 147
131 Check this worked: 148 Check this worked:
132 149
133 $ tar -tzf tmhmm_signalp_etc.tar.gz 150 $ tar -tzf tmhmm_signalp_etc.tar.gz
134 tools/protein_analysis/LICENSE 151 tools/protein_analysis/LICENSE
137 tools/protein_analysis/seq_analysis_utils.py 154 tools/protein_analysis/seq_analysis_utils.py
138 tools/protein_analysis/signalp3.xml 155 tools/protein_analysis/signalp3.xml
139 tools/protein_analysis/signalp3.py 156 tools/protein_analysis/signalp3.py
140 tools/protein_analysis/tmhmm2.xml 157 tools/protein_analysis/tmhmm2.xml
141 tools/protein_analysis/tmhmm2.py 158 tools/protein_analysis/tmhmm2.py
159 tools/protein_analysis/promoter2.xml
160 tools/protein_analysis/promoter2.py
142 tools/protein_analysis/wolf_psort.xml 161 tools/protein_analysis/wolf_psort.xml
143 tools/protein_analysis/wolf_psort.py 162 tools/protein_analysis/wolf_psort.py
144 tools/protein_analysis/rxlr_motifs.xml 163 tools/protein_analysis/rxlr_motifs.xml
145 tools/protein_analysis/rxrl_motifs.py 164 tools/protein_analysis/rxrl_motifs.py
146 test-data/four_human_proteins.fasta 165 test-data/four_human_proteins.fasta