Mercurial > repos > peterjc > tmhmm_and_signalp

annotate tools/protein_analysis/README @ 13:c6e5a737d3a0 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded v0.2.2, was missing some test files
author peterjc
date Mon, 22 Apr 2013 11:46:20 -0400
parents 7c1eda453701
children a705202ae2a7
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
ef7ceca37e3f Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository
peterjc
parents: 4
diff changeset
1 This package contains Galaxy wrappers for a selection of standalone command
ef7ceca37e3f Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository
peterjc
parents: 4
diff changeset
2 line protein analysis tools:
ef7ceca37e3f Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository
peterjc
parents: 4
diff changeset
3
7
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents: 6
diff changeset
4 * SignalP 3.0, THMHMM 2.0, Promoter 2.0 from the Center for Biological
5
ef7ceca37e3f Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository
peterjc
parents: 4
diff changeset
5 Sequence Analysis at the Technical University of Denmark,
ef7ceca37e3f Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository
peterjc
parents: 4
diff changeset
6 http://www.cbs.dtu.dk/cbs/
ef7ceca37e3f Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository
peterjc
parents: 4
diff changeset
7
ef7ceca37e3f Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository
peterjc
parents: 4
diff changeset
8 * WoLF PSORT v0.2 from http://wolfpsort.org/
ef7ceca37e3f Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository
peterjc
parents: 4
diff changeset
9
8
391a142c1e60 Uploaded
peterjc
parents: 7
diff changeset
10 * PSORTb v3 from http://www.psort.org/downloads/index.html
391a142c1e60 Uploaded
peterjc
parents: 7
diff changeset
11
6
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents: 5
diff changeset
12 Also, the RXLR motif tool uses SignalP 3.0 and HMMER 2.3.2 internally.
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents: 5
diff changeset
13
5
ef7ceca37e3f Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository
peterjc
parents: 4
diff changeset
14 To use these Galaxy wrappers you must first install the command line tools.
8
391a142c1e60 Uploaded
peterjc
parents: 7
diff changeset
15 At the time of writing they are all free for academic use, or open source.
5
ef7ceca37e3f Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository
peterjc
parents: 4
diff changeset
16
10
7c1eda453701 Uploaded revised v0.2.0 with clearer acknowledgement of contributors
peterjc
parents: 9
diff changeset
17 These wrappers are copyright 2010-2013 by Peter Cock, James Hutton Institute
5
ef7ceca37e3f Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository
peterjc
parents: 4
diff changeset
18 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
10
7c1eda453701 Uploaded revised v0.2.0 with clearer acknowledgement of contributors
peterjc
parents: 9
diff changeset
19 Contributions/revisions copyright 2011 Konrad Paszkiewicz. All rights reserved.
7
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents: 6
diff changeset
20 See the included LICENCE file for details (an MIT style open source licence).
0
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
21
13
c6e5a737d3a0 Uploaded v0.2.2, was missing some test files
peterjc
parents: 10
diff changeset
22
5
ef7ceca37e3f Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository
peterjc
parents: 4
diff changeset
23 Requirements
ef7ceca37e3f Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository
peterjc
parents: 4
diff changeset
24 ============
ef7ceca37e3f Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository
peterjc
parents: 4
diff changeset
25
ef7ceca37e3f Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository
peterjc
parents: 4
diff changeset
26 First install those command line tools you wish to use the wrappers for:
ef7ceca37e3f Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository
peterjc
parents: 4
diff changeset
27
ef7ceca37e3f Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository
peterjc
parents: 4
diff changeset
28 1. Install the command line version of SignalP 3.0 and ensure "signalp" is
ef7ceca37e3f Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository
peterjc
parents: 4
diff changeset
29 on the PATH, see: http://www.cbs.dtu.dk/services/SignalP/
0
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
30
5
ef7ceca37e3f Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository
peterjc
parents: 4
diff changeset
31 2. Install the command line version of TMHMM 2.0 and ensure "tmhmm" is on
ef7ceca37e3f Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository
peterjc
parents: 4
diff changeset
32 the PATH, see: http://www.cbs.dtu.dk/services/TMHMM/
ef7ceca37e3f Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository
peterjc
parents: 4
diff changeset
33
7
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents: 6
diff changeset
34 3. Install the command line version of Promoter 2.0 and ensure "promoter" is
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents: 6
diff changeset
35 on the PATH, see: http://www.cbs.dtu.dk/services/Promoter
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents: 6
diff changeset
36
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents: 6
diff changeset
37 4. Install the WoLF PSORT v0.2 package, and ensure "runWolfPsortSummary"
5
ef7ceca37e3f Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository
peterjc
parents: 4
diff changeset
38 is on the PATH (we use an extra wrapper script to change to the WoLF PSORT
ef7ceca37e3f Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository
peterjc
parents: 4
diff changeset
39 directory, run runWolfPsortSummary, and then change back to the original
ef7ceca37e3f Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository
peterjc
parents: 4
diff changeset
40 directory), see: http://wolfpsort.org/WoLFPSORT_package/version0.2/
ef7ceca37e3f Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository
peterjc
parents: 4
diff changeset
41
7
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents: 6
diff changeset
42 5. Install hmmsearch from HMMER 2.3.2 (the last stable release of HMMER 2)
6
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents: 5
diff changeset
43 but put it on the path under the name hmmsearch2 (allowing it to co-exist
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents: 5
diff changeset
44 with HMMER 3), or edit rlxr_motif.py accordingly.
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents: 5
diff changeset
45
5
ef7ceca37e3f Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository
peterjc
parents: 4
diff changeset
46 Verify each of the tools is installed and working from the command line
7
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents: 6
diff changeset
47 (when logged in as the Galaxy user if appropriate).
0
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
48
13
c6e5a737d3a0 Uploaded v0.2.2, was missing some test files
peterjc
parents: 10
diff changeset
49
7
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents: 6
diff changeset
50 Manual Installation
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents: 6
diff changeset
51 ===================
0
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
52
5
ef7ceca37e3f Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository
peterjc
parents: 4
diff changeset
53 1. Create a folder tools/protein_analysis under your Galaxy installation.
7
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents: 6
diff changeset
54 This folder name is not critical, and can be changed if desired - you
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents: 6
diff changeset
55 must update the paths used in tool_conf.xml to match.
0
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
56
5
ef7ceca37e3f Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository
peterjc
parents: 4
diff changeset
57 2. Copy/move the following files (from this archive) there:
0
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
58
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
59 tmhmm2.xml (Galaxy tool definition)
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
60 tmhmm2.py (Python wrapper script)
5
ef7ceca37e3f Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository
peterjc
parents: 4
diff changeset
61
0
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
62 signalp3.xml (Galaxy tool definition)
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
63 signalp3.py (Python wrapper script)
5
ef7ceca37e3f Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository
peterjc
parents: 4
diff changeset
64
7
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents: 6
diff changeset
65 promoter2.xml (Galaxy tool definition)
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents: 6
diff changeset
66 promoter2.py (Python wrapper script)
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents: 6
diff changeset
67
8
391a142c1e60 Uploaded
peterjc
parents: 7
diff changeset
68 psortb.xml (Galaxy tool definition)
391a142c1e60 Uploaded
peterjc
parents: 7
diff changeset
69 psortb.py (Python wrapper script)
391a142c1e60 Uploaded
peterjc
parents: 7
diff changeset
70
5
ef7ceca37e3f Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository
peterjc
parents: 4
diff changeset
71 wolf_psort.xml (Galaxy tool definition)
ef7ceca37e3f Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository
peterjc
parents: 4
diff changeset
72 wolf_psort.py (Python wrapper script)
ef7ceca37e3f Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository
peterjc
parents: 4
diff changeset
73
6
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents: 5
diff changeset
74 rxlr_motifs.xml (Galaxy tool definition)
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents: 5
diff changeset
75 rxlr_motifs.py (Python script)
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents: 5
diff changeset
76
0
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
77 seq_analysis_utils.py (shared Python code)
7
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents: 6
diff changeset
78 LICENCE
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents: 6
diff changeset
79 README (this file)
0
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
80
5
ef7ceca37e3f Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository
peterjc
parents: 4
diff changeset
81 3. Edit your Galaxy conjuration file tool_conf.xml (to use the tools) AND
ef7ceca37e3f Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository
peterjc
parents: 4
diff changeset
82 also tool_conf.xml.sample (to run the tests) to include the new tools
0
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
83 by adding:
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
84
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
85 <section name="Protein sequence analysis" id="protein_analysis">
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
86 <tool file="protein_analysis/tmhmm2.xml" />
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
87 <tool file="protein_analysis/signalp3.xml" />
8
391a142c1e60 Uploaded
peterjc
parents: 7
diff changeset
88 <tool file="protein_analysis/psortb.xml" />
5
ef7ceca37e3f Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository
peterjc
parents: 4
diff changeset
89 <tool file="protein_analysis/wolf_psort.xml" />
6
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents: 5
diff changeset
90 <tool file="protein_analysis/rxlr_motifs.xml" />
0
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
91 </section>
7
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents: 6
diff changeset
92 <section name="Nucleotide sequence analysis" id="nucleotide_analysis">
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents: 6
diff changeset
93 <tool file="protein_analysis/promoter2.xml" />
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents: 6
diff changeset
94 </section>
0
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
95
5
ef7ceca37e3f Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository
peterjc
parents: 4
diff changeset
96 Leave out the lines for any tools you do not wish to use in Galaxy.
ef7ceca37e3f Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository
peterjc
parents: 4
diff changeset
97
13
c6e5a737d3a0 Uploaded v0.2.2, was missing some test files
peterjc
parents: 10
diff changeset
98 4. Copy/move the test-data files (from this archive) to Galaxy's
c6e5a737d3a0 Uploaded v0.2.2, was missing some test files
peterjc
parents: 10
diff changeset
99 subfolder test-data.
0
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
100
5
ef7ceca37e3f Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository
peterjc
parents: 4
diff changeset
101 5. Run the Galaxy functional tests for these new wrappers with:
0
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
102
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
103 ./run_functional_tests.sh -id tmhmm2
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
104 ./run_functional_tests.sh -id signalp3
8
391a142c1e60 Uploaded
peterjc
parents: 7
diff changeset
105 ./run_functional_tests.sh -id Psortb
391a142c1e60 Uploaded
peterjc
parents: 7
diff changeset
106 ./run_functional_tests.sh -id rxlr_motifs
0
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
107
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
108 Alternatively, this should work (assuming you left the name and id as shown in
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
109 the XML file tool_conf.xml.sample):
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
110
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
111 ./run_functional_tests.sh -sid Protein_sequence_analysis-protein_analysis
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
112
8
391a142c1e60 Uploaded
peterjc
parents: 7
diff changeset
113 To check the section ID expected, use ./run_functional_tests.sh -list
391a142c1e60 Uploaded
peterjc
parents: 7
diff changeset
114
5
ef7ceca37e3f Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository
peterjc
parents: 4
diff changeset
115 6. Restart Galaxy and check the new tools are shown and work.
1
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
116
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
117
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
118 History
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
119 =======
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
120
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
121 v0.0.1 - Initial release
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
122 v0.0.2 - Corrected some typos in the help text
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
123 - Renamed test output file to use Galaxy convention of *.tabular
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
124 v0.0.3 - Check for tmhmm2 silent failures (no output)
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
125 - Additional unit tests
2
747cec3192d3 Migrated tool version 0.0.5 from old tool shed archive to new tool shed repository
peterjc
parents: 1
diff changeset
126 v0.0.4 - Ignore comment lines in tmhmm2 output.
747cec3192d3 Migrated tool version 0.0.5 from old tool shed archive to new tool shed repository
peterjc
parents: 1
diff changeset
127 v0.0.5 - Explicitly request tmhmm short output (may not be the default)
3
fe10f448d641 Migrated tool version 0.0.6 from old tool shed archive to new tool shed repository
peterjc
parents: 2
diff changeset
128 v0.0.6 - Improvement to how sub-jobs are run (should be faster)
4
1426b2bae76d Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
peterjc
parents: 3
diff changeset
129 v0.0.7 - Change SignalP default truncation from 60 to 70 to match the
1426b2bae76d Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
peterjc
parents: 3
diff changeset
130 SignalP webservice.
5
ef7ceca37e3f Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository
peterjc
parents: 4
diff changeset
131 v0.0.8 - Added WoLF PSORT wrapper to the suite.
6
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents: 5
diff changeset
132 v0.0.9 - Added our RXLR motifs tool to the suite.
7
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents: 6
diff changeset
133 v0.1.0 - Added Promoter 2.0 wrapper (similar to SignalP & TMHMM wrappers)
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents: 6
diff changeset
134 - Support Galaxy's <parallelism> tag for SignalP, TMHMM & Promoter
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents: 6
diff changeset
135 v0.1.1 - Fixed an error in the header of the tabular output from Promoter
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents: 6
diff changeset
136 v0.1.2 - Use the new <stdio> settings in the XML wrappers to catch errors
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents: 6
diff changeset
137 - Use SGE style $NSLOTS for thread count (otherwise default to 4)
9
9a9971a1e55e Uploaded v0.2.0a
peterjc
parents: 8
diff changeset
138 v0.1.3 - Added missing file whisson_et_al_rxlr_eer_cropped.hmm to Tool Shed
8
391a142c1e60 Uploaded
peterjc
parents: 7
diff changeset
139 v0.2.0 - Added PSORTb wrapper to the suite, based on earlier work
391a142c1e60 Uploaded
peterjc
parents: 7
diff changeset
140 contributed by Konrad Paszkiewicz.
13
c6e5a737d3a0 Uploaded v0.2.2, was missing some test files
peterjc
parents: 10
diff changeset
141 v0.2.1 - Use a script to create the Tool Shed tar-ball (removed some stray
c6e5a737d3a0 Uploaded v0.2.2, was missing some test files
peterjc
parents: 10
diff changeset
142 files accidentally included previously via a wildcard).
c6e5a737d3a0 Uploaded v0.2.2, was missing some test files
peterjc
parents: 10
diff changeset
143 v0.2.2 - Include missing test files.
4
1426b2bae76d Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
peterjc
parents: 3
diff changeset
144
1
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
145
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
146 Developers
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
147 ==========
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
148
3
fe10f448d641 Migrated tool version 0.0.6 from old tool shed archive to new tool shed repository
peterjc
parents: 2
diff changeset
149 This script and other tools are being developed on the following hg branch:
fe10f448d641 Migrated tool version 0.0.6 from old tool shed archive to new tool shed repository
peterjc
parents: 2
diff changeset
150 http://bitbucket.org/peterjc/galaxy-central/src/tools
fe10f448d641 Migrated tool version 0.0.6 from old tool shed archive to new tool shed repository
peterjc
parents: 2
diff changeset
151
fe10f448d641 Migrated tool version 0.0.6 from old tool shed archive to new tool shed repository
peterjc
parents: 2
diff changeset
152 This incorporates the previously used hg branch:
1
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
153 http://bitbucket.org/peterjc/galaxy-central/src/seq_analysis
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
154
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
155 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
156 the following command from the Galaxy root folder:
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
157
13
c6e5a737d3a0 Uploaded v0.2.2, was missing some test files
peterjc
parents: 10
diff changeset
158 $ ./tools/protein_analysis/make_tmhmm_and_signalp.sh
1
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
159
13
c6e5a737d3a0 Uploaded v0.2.2, was missing some test files
peterjc
parents: 10
diff changeset
160 This simplifies ensuring a consistent set of files is bundled each time,
c6e5a737d3a0 Uploaded v0.2.2, was missing some test files
peterjc
parents: 10
diff changeset
161 including all the relevant test files.