Mercurial > repos > peterjc > tmhmm_and_signalp

annotate tools/protein_analysis/README @ 15:6abd809cefdd draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded v0.2.4, added unit tests for Promoter 2
author peterjc
date Thu, 25 Apr 2013 12:25:52 -0400
parents 6365217cd3de
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
0f1c61998b22 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
0f1c61998b22 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:
0f1c61998b22 Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository
peterjc
parents: 4
diff changeset
3
7
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers.
peterjc
parents: 6
diff changeset
4 * SignalP 3.0, THMHMM 2.0, Promoter 2.0 from the Center for Biological
5
0f1c61998b22 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,
0f1c61998b22 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/
0f1c61998b22 Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository
peterjc
parents: 4
diff changeset
7
0f1c61998b22 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/
0f1c61998b22 Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository
peterjc
parents: 4
diff changeset
9
11
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz)
peterjc
parents: 10
diff changeset
10 * PSORTb v3 from http://www.psort.org/downloads/index.html
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz)
peterjc
parents: 10
diff changeset
11
6
a290c6d4e658 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.
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents: 5
diff changeset
13
5
0f1c61998b22 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.
11
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz)
peterjc
parents: 10
diff changeset
15 At the time of writing they are all free for academic use, or open source.
5
0f1c61998b22 Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository
peterjc
parents: 4
diff changeset
16
11
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz)
peterjc
parents: 10
diff changeset
17 These wrappers are copyright 2010-2013 by Peter Cock, James Hutton Institute
5
0f1c61998b22 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.
11
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz)
peterjc
parents: 10
diff changeset
19 Contributions/revisions copyright 2011 Konrad Paszkiewicz. All rights reserved.
7
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers.
peterjc
parents: 6
diff changeset
20 See the included LICENCE file for details (an MIT style open source licence).
0
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
21
13
dc958c2a963a Uploaded v0.2.2, adds missing test files
peterjc
parents: 11
diff changeset
22
5
0f1c61998b22 Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository
peterjc
parents: 4
diff changeset
23 Requirements
0f1c61998b22 Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository
peterjc
parents: 4
diff changeset
24 ============
0f1c61998b22 Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository
peterjc
parents: 4
diff changeset
25
0f1c61998b22 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:
0f1c61998b22 Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository
peterjc
parents: 4
diff changeset
27
0f1c61998b22 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
0f1c61998b22 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
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
30
5
0f1c61998b22 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
0f1c61998b22 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/
0f1c61998b22 Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository
peterjc
parents: 4
diff changeset
33
7
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers.
peterjc
parents: 6
diff changeset
34 3. Install the command line version of Promoter 2.0 and ensure "promoter" is
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers.
peterjc
parents: 6
diff changeset
35 on the PATH, see: http://www.cbs.dtu.dk/services/Promoter
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers.
peterjc
parents: 6
diff changeset
36
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers.
peterjc
parents: 6
diff changeset
37 4. Install the WoLF PSORT v0.2 package, and ensure "runWolfPsortSummary"
5
0f1c61998b22 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
0f1c61998b22 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
0f1c61998b22 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/
0f1c61998b22 Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository
peterjc
parents: 4
diff changeset
41
7
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers.
peterjc
parents: 6
diff changeset
42 5. Install hmmsearch from HMMER 2.3.2 (the last stable release of HMMER 2)
6
a290c6d4e658 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
a290c6d4e658 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.
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents: 5
diff changeset
45
5
0f1c61998b22 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
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers.
peterjc
parents: 6
diff changeset
47 (when logged in as the Galaxy user if appropriate).
0
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
48
13
dc958c2a963a Uploaded v0.2.2, adds missing test files
peterjc
parents: 11
diff changeset
49
7
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers.
peterjc
parents: 6
diff changeset
50 Manual Installation
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers.
peterjc
parents: 6
diff changeset
51 ===================
0
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
52
5
0f1c61998b22 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
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers.
peterjc
parents: 6
diff changeset
54 This folder name is not critical, and can be changed if desired - you
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers.
peterjc
parents: 6
diff changeset
55 must update the paths used in tool_conf.xml to match.
0
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
56
5
0f1c61998b22 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
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
58
bca9bc7fdaef 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)
bca9bc7fdaef 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
0f1c61998b22 Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository
peterjc
parents: 4
diff changeset
61
0
bca9bc7fdaef 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)
bca9bc7fdaef 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
0f1c61998b22 Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository
peterjc
parents: 4
diff changeset
64
7
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers.
peterjc
parents: 6
diff changeset
65 promoter2.xml (Galaxy tool definition)
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers.
peterjc
parents: 6
diff changeset
66 promoter2.py (Python wrapper script)
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers.
peterjc
parents: 6
diff changeset
67
11
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz)
peterjc
parents: 10
diff changeset
68 psortb.xml (Galaxy tool definition)
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz)
peterjc
parents: 10
diff changeset
69 psortb.py (Python wrapper script)
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz)
peterjc
parents: 10
diff changeset
70
5
0f1c61998b22 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)
0f1c61998b22 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)
0f1c61998b22 Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository
peterjc
parents: 4
diff changeset
73
6
a290c6d4e658 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)
a290c6d4e658 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)
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents: 5
diff changeset
76
0
bca9bc7fdaef 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
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers.
peterjc
parents: 6
diff changeset
78 LICENCE
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers.
peterjc
parents: 6
diff changeset
79 README (this file)
0
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
80
5
0f1c61998b22 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
0f1c61998b22 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
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
83 by adding:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
84
bca9bc7fdaef 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">
bca9bc7fdaef 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" />
bca9bc7fdaef 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" />
11
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz)
peterjc
parents: 10
diff changeset
88 <tool file="protein_analysis/psortb.xml" />
5
0f1c61998b22 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
a290c6d4e658 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
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
91 </section>
7
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers.
peterjc
parents: 6
diff changeset
92 <section name="Nucleotide sequence analysis" id="nucleotide_analysis">
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers.
peterjc
parents: 6
diff changeset
93 <tool file="protein_analysis/promoter2.xml" />
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers.
peterjc
parents: 6
diff changeset
94 </section>
0
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
95
5
0f1c61998b22 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.
0f1c61998b22 Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository
peterjc
parents: 4
diff changeset
97
13
dc958c2a963a Uploaded v0.2.2, adds missing test files
peterjc
parents: 11
diff changeset
98 4. Copy/move the test-data files (from this archive) to Galaxy's
dc958c2a963a Uploaded v0.2.2, adds missing test files
peterjc
parents: 11
diff changeset
99 subfolder test-data.
0
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
100
5
0f1c61998b22 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
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
102
bca9bc7fdaef 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
bca9bc7fdaef 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
11
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz)
peterjc
parents: 10
diff changeset
105 ./run_functional_tests.sh -id Psortb
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz)
peterjc
parents: 10
diff changeset
106 ./run_functional_tests.sh -id rxlr_motifs
0
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
107
bca9bc7fdaef 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
bca9bc7fdaef 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):
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
110
bca9bc7fdaef 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
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
112
11
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz)
peterjc
parents: 10
diff changeset
113 To check the section ID expected, use ./run_functional_tests.sh -list
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz)
peterjc
parents: 10
diff changeset
114
5
0f1c61998b22 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
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
116
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
117
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
118 History
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
119 =======
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
120
3ff1dcbb9440 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
3ff1dcbb9440 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
3ff1dcbb9440 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
3ff1dcbb9440 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)
3ff1dcbb9440 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
6901298ac16c 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.
6901298ac16c 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
f3b373a41f81 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
81caef04ce8b 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
81caef04ce8b 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
0f1c61998b22 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
a290c6d4e658 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
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers.
peterjc
parents: 6
diff changeset
133 v0.1.0 - Added Promoter 2.0 wrapper (similar to SignalP & TMHMM wrappers)
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers.
peterjc
parents: 6
diff changeset
134 - Support Galaxy's <parallelism> tag for SignalP, TMHMM & Promoter
8
976a5f2833cd Uploaded v0.1.1 of the bundle, which fixes an error in the header of the tabular output produced for Promoter 2.0
peterjc
parents: 7
diff changeset
135 v0.1.1 - Fixed an error in the header of the tabular output from Promoter
9
e52220a9ddad Uploaded v0.1.2
peterjc
parents: 8
diff changeset
136 v0.1.2 - Use the new <stdio> settings in the XML wrappers to catch errors
e52220a9ddad Uploaded v0.1.2
peterjc
parents: 8
diff changeset
137 - Use SGE style $NSLOTS for thread count (otherwise default to 4)
10
09ff180d1615 Uploaded v0.1.3 with missing HMM file for RXLR tool included.
peterjc
parents: 9
diff changeset
138 v0.1.3 - Added missing file whisson_et_al_rxlr_eer_cropped.hmm to Tool Shed
11
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz)
peterjc
parents: 10
diff changeset
139 v0.2.0 - Added PSORTb wrapper to the suite, based on earlier work
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz)
peterjc
parents: 10
diff changeset
140 contributed by Konrad Paszkiewicz.
13
dc958c2a963a Uploaded v0.2.2, adds missing test files
peterjc
parents: 11
diff changeset
141 v0.2.1 - Use a script to create the Tool Shed tar-ball (removed some stray
dc958c2a963a Uploaded v0.2.2, adds missing test files
peterjc
parents: 11
diff changeset
142 files accidentally included previously via a wildcard).
dc958c2a963a Uploaded v0.2.2, adds missing test files
peterjc
parents: 11
diff changeset
143 v0.2.2 - Include missing test files.
14
6365217cd3de Uploaded v0.2.3, adds unit tests for WoLF PSORT
peterjc
parents: 13
diff changeset
144 v0.2.3 - Added unit tests for WoLF PSORT.
15
6abd809cefdd Uploaded v0.2.4, added unit tests for Promoter 2
peterjc
parents: 14
diff changeset
145 v0.2.4 - Added unit tests for Promoter 2
9
e52220a9ddad Uploaded v0.1.2
peterjc
parents: 8
diff changeset
146
1
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
147
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
148 Developers
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
149 ==========
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
150
3
f3b373a41f81 Migrated tool version 0.0.6 from old tool shed archive to new tool shed repository
peterjc
parents: 2
diff changeset
151 This script and other tools are being developed on the following hg branch:
f3b373a41f81 Migrated tool version 0.0.6 from old tool shed archive to new tool shed repository
peterjc
parents: 2
diff changeset
152 http://bitbucket.org/peterjc/galaxy-central/src/tools
f3b373a41f81 Migrated tool version 0.0.6 from old tool shed archive to new tool shed repository
peterjc
parents: 2
diff changeset
153
f3b373a41f81 Migrated tool version 0.0.6 from old tool shed archive to new tool shed repository
peterjc
parents: 2
diff changeset
154 This incorporates the previously used hg branch:
1
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
155 http://bitbucket.org/peterjc/galaxy-central/src/seq_analysis
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
156
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
157 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
158 the following command from the Galaxy root folder:
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
159
13
dc958c2a963a Uploaded v0.2.2, adds missing test files
peterjc
parents: 11
diff changeset
160 $ ./tools/protein_analysis/make_tmhmm_and_signalp.sh
1
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
161
13
dc958c2a963a Uploaded v0.2.2, adds missing test files
peterjc
parents: 11
diff changeset
162 This simplifies ensuring a consistent set of files is bundled each time,
dc958c2a963a Uploaded v0.2.2, adds missing test files
peterjc
parents: 11
diff changeset
163 including all the relevant test files.