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comparison tools/protein_analysis/README @ 5:0f1c61998b22

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Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository
author peterjc
date Tue, 07 Jun 2011 18:06:27 -0400
parents 81caef04ce8b
children a290c6d4e658
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4:81caef04ce8b 5:0f1c61998b22
1 This package contains Galaxy wrappers for two standalone command line protein 1 This package contains Galaxy wrappers for a selection of standalone command
2 analysis tools (SignalP 3.0 and THMHMM 2.0) from the Center for Biological 2 line protein analysis tools:
3 Sequence Analysis at the Technical University of Denmark,
4 http://www.cbs.dtu.dk/cbs/
5 3
6 To use these Galaxy wrappers you must first install the CBS command line 4 * SignalP 3.0 and THMHMM 2.0, from the Center for Biological
7 tools. At the time of writing both SignalP 3.0 and TMHMM 2.0 are free for 5 Sequence Analysis at the Technical University of Denmark,
8 academic use. 6 http://www.cbs.dtu.dk/cbs/
9 7
10 These wrappers are copyright 2010 by Peter Cock, SCRI, UK. All rights 8 * WoLF PSORT v0.2 from http://wolfpsort.org/
11 reserved. See the included LICENCE file for details. 9
10 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.
12
13 These wrappers are copyright 2010-2011 by Peter Cock, James Hutton Institute
14 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
15 See the included LICENCE file for details.
16
17 Requirements
18 ============
19
20 First install those command line tools you wish to use the wrappers for:
21
22 1. Install the command line version of SignalP 3.0 and ensure "signalp" is
23 on the PATH, see: http://www.cbs.dtu.dk/services/SignalP/
24
25 2. Install the command line version of TMHMM 2.0 and ensure "tmhmm" is on
26 the PATH, see: http://www.cbs.dtu.dk/services/TMHMM/
27
28 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
30 directory, run runWolfPsortSummary, and then change back to the original
31 directory), see: http://wolfpsort.org/WoLFPSORT_package/version0.2/
32
33 Verify each of the tools is installed and working from the command line
34 (when logged in at the Galaxy user if appropriate).
12 35
13 Installation 36 Installation
14 ============ 37 ============
15 38
16 1. Install the command line version of SignalP 3.0 and ensure it is on the 39 1. Create a folder tools/protein_analysis under your Galaxy installation.
17 PATH, see: http://www.cbs.dtu.dk/services/SignalP/
18 40
19 2. Install the command line version of TMHMM 2.0 and ensure it is on the 41 2. Copy/move the following files (from this archive) there:
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 42
26 tmhmm2.xml (Galaxy tool definition) 43 tmhmm2.xml (Galaxy tool definition)
27 tmhmm2.py (Python wrapper script) 44 tmhmm2.py (Python wrapper script)
45
28 signalp3.xml (Galaxy tool definition) 46 signalp3.xml (Galaxy tool definition)
29 signalp3.py (Python wrapper script) 47 signalp3.py (Python wrapper script)
48
49 wolf_psort.xml (Galaxy tool definition)
50 wolf_psort.py (Python wrapper script)
51
30 seq_analysis_utils.py (shared Python code) 52 seq_analysis_utils.py (shared Python code)
31 README (optional) 53 README (optional)
32 54
33 5. Edit your Galaxy conjuration file tool_conf.xml (to use the tools) AND 55 3. 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 56 also tool_conf.xml.sample (to run the tests) to include the new tools
35 by adding: 57 by adding:
36 58
37 <section name="Protein sequence analysis" id="protein_analysis"> 59 <section name="Protein sequence analysis" id="protein_analysis">
38 <tool file="protein_analysis/tmhmm2.xml" /> 60 <tool file="protein_analysis/tmhmm2.xml" />
39 <tool file="protein_analysis/signalp3.xml" /> 61 <tool file="protein_analysis/signalp3.xml" />
62 <tool file="protein_analysis/wolf_psort.xml" />
40 </section> 63 </section>
41 64
42 6. Copy/move the following test files (from these archive) to Galaxy 65 Leave out the lines for any tools you do not wish to use in Galaxy.
66
67 4. Copy/move the following test files (from these archive) to Galaxy
43 subfolder test-data: 68 subfolder test-data:
44 69
45 four_human_proteins.fasta 70 four_human_proteins.fasta
46 four_human_proteins_signalp3.tabular 71 four_human_proteins_signalp3.tabular
47 four_human_proteins_tmhmm2.tabular 72 four_human_proteins_tmhmm2.tabular
48 empty.fasta 73 empty.fasta
49 empty_tmhmm2.tabular 74 empty_tmhmm2.tabular
50 empty_signalp3.tabular 75 empty_signalp3.tabular
51 76
52 7. Run the Galaxy functional tests for these new wrappers with: 77 5. Run the Galaxy functional tests for these new wrappers with:
53 78
54 ./run_functional_tests.sh -id tmhmm2 79 ./run_functional_tests.sh -id tmhmm2
55 ./run_functional_tests.sh -id signalp3 80 ./run_functional_tests.sh -id signalp3
56 81
57 Alternatively, this should work (assuming you left the name and id as shown in 82 Alternatively, this should work (assuming you left the name and id as shown in
58 the XML file tool_conf.xml.sample): 83 the XML file tool_conf.xml.sample):
59 84
60 ./run_functional_tests.sh -sid Protein_sequence_analysis-protein_analysis 85 ./run_functional_tests.sh -sid Protein_sequence_analysis-protein_analysis
61 86
62 8. Restart Galaxy and check the new tools are shown and work. 87 6. Restart Galaxy and check the new tools are shown and work.
63 88
64 89
65 History 90 History
66 ======= 91 =======
67 92
73 v0.0.4 - Ignore comment lines in tmhmm2 output. 98 v0.0.4 - Ignore comment lines in tmhmm2 output.
74 v0.0.5 - Explicitly request tmhmm short output (may not be the default) 99 v0.0.5 - Explicitly request tmhmm short output (may not be the default)
75 v0.0.6 - Improvement to how sub-jobs are run (should be faster) 100 v0.0.6 - Improvement to how sub-jobs are run (should be faster)
76 v0.0.7 - Change SignalP default truncation from 60 to 70 to match the 101 v0.0.7 - Change SignalP default truncation from 60 to 70 to match the
77 SignalP webservice. 102 SignalP webservice.
103 v0.0.8 - Added WoLF PSORT wrapper to the suite.
78 104
79 105
80 Developers 106 Developers
81 ========== 107 ==========
82 108
87 http://bitbucket.org/peterjc/galaxy-central/src/seq_analysis 113 http://bitbucket.org/peterjc/galaxy-central/src/seq_analysis
88 114
89 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use 115 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use
90 the following command from the Galaxy root folder: 116 the following command from the Galaxy root folder:
91 117
92 tar -czf tmhmm_and_signalp.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 test-data/four_human_proteins.* test-data/empty.fasta test-data/empty_tmhmm2.tabular test-data/empty_signalp3.tabular 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
93 119
94 Check this worked: 120 Check this worked:
95 121
96 $ tar -tzf tmhmm_and_signalp.tar.gz 122 $ tar -tzf tmhmm_signalp_wolfpsort.tar.gz
97 tools/protein_analysis/LICENSE 123 tools/protein_analysis/LICENSE
98 tools/protein_analysis/README 124 tools/protein_analysis/README
99 tools/protein_analysis/suite_config.xml 125 tools/protein_analysis/suite_config.xml
100 tools/protein_analysis/seq_analysis_utils.py 126 tools/protein_analysis/seq_analysis_utils.py
101 tools/protein_analysis/signalp3.xml 127 tools/protein_analysis/signalp3.xml
102 tools/protein_analysis/signalp3.py 128 tools/protein_analysis/signalp3.py
103 tools/protein_analysis/tmhmm2.xml 129 tools/protein_analysis/tmhmm2.xml
104 tools/protein_analysis/tmhmm2.py 130 tools/protein_analysis/tmhmm2.py
131 tools/protein_analysis/wolf_psort.xml
132 tools/protein_analysis/wolf_psort.py
105 test-data/four_human_proteins.fasta 133 test-data/four_human_proteins.fasta
106 test-data/four_human_proteins.signalp3.tabular 134 test-data/four_human_proteins.signalp3.tabular
107 test-data/four_human_proteins.tmhmm2.tabular 135 test-data/four_human_proteins.tmhmm2.tabular
108 test-data/empty.fasta 136 test-data/empty.fasta
109 test-data/empty_tmhmm2.tabular 137 test-data/empty_tmhmm2.tabular