Mercurial > repos > peterjc > tmhmm_and_signalp

annotate tools/protein_analysis/README @ 1:3ff1dcbb9440

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
author peterjc
date Tue, 07 Jun 2011 18:04:05 -0400
parents bca9bc7fdaef
children 6901298ac16c
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
1 This package contains Galaxy wrappers for two standalone command line protein
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
2 analysis tools (SignalP 3.0 and THMHMM 2.0) from the Center for Biological
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
3 Sequence Analysis at the Technical University of Denmark,
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
4 http://www.cbs.dtu.dk/cbs/
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
5
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
6 To use these Galaxy wrappers you must first install the CBS command line
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
7 tools. At the time of writing both SignalP 3.0 and TMHMM 2.0 are free for
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
8 academic use.
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
9
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
10 These wrappers are copyright 2010 by Peter Cock, SCRI, UK. All rights
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
11 reserved. See the included LICENCE file for details.
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
12
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
13 Installation
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
14 ============
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
15
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
16 1. Install the command line version of SignalP 3.0 and ensure it is on the
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
17 PATH, see: http://www.cbs.dtu.dk/services/SignalP/
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
18
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
19 2. Install the command line version of TMHMM 2.0 and ensure it is on the
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
20 PATH, see: http://www.cbs.dtu.dk/services/TMHMM/
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
21
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
22 3. Create a folder tools/protein_analysis under your Galaxy installation.
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
23
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
24 4. Copy/move the following files (from this archive) there:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
25
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
26 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
27 tmhmm2.py (Python wrapper script)
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
28 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
29 signalp3.py (Python wrapper script)
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
30 seq_analysis_utils.py (shared Python code)
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
31 README (optional)
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
32
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
33 5. Edit your Galaxy conjuration file tool_conf.xml (to use the tools) AND
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
34 also tool_conf.xml.sample (to run the tests) to include the two new tools
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
35 by adding:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
36
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
37 <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
38 <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
39 <tool file="protein_analysis/signalp3.xml" />
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
40 </section>
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
41
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
42 6. Copy/move the following test files (from these archive) to Galaxy
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
43 subfolder test-data:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
44
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
45 four_human_proteins.fasta
1
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
46 four_human_proteins_signalp3.tabular
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
47 four_human_proteins_tmhmm2.tabular
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
48 empty.fasta
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
49 empty_tmhmm2.tabular
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
50 empty_signalp3.tabular
0
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
51
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
52 7. Run the Galaxy functional tests for these new wrappers with:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
53
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
54 ./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
55 ./run_functional_tests.sh -id signalp3
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
56
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
57 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
58 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
59
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
60 ./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
61
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
62 8. 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
63
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
64
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
65 History
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
66 =======
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
67
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
68 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
69 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
70 - 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
71 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
72 - Additional unit tests
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
73
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
74 Developers
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
75 ==========
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
76
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
77 These wrappers are currently being developed on the following hg branch:
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
78 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
79
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
80 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
81 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
82
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
83 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
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
84
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
85 Check this worked:
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
86
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
87 $ tar -tzf tmhmm_and_signalp.tar.gz
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
88 tools/protein_analysis/LICENSE
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
89 tools/protein_analysis/README
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
90 tools/protein_analysis/suite_config.xml
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
91 tools/protein_analysis/seq_analysis_utils.py
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
92 tools/protein_analysis/signalp3.xml
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
93 tools/protein_analysis/signalp3.py
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
94 tools/protein_analysis/tmhmm2.xml
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
95 tools/protein_analysis/tmhmm2.py
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
96 test-data/four_human_proteins.fasta
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
97 test-data/four_human_proteins.signalp3.tabular
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
98 test-data/four_human_proteins.tmhmm2.tabular
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
99 test-data/empty.fasta
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
100 test-data/empty_tmhmm2.tabular
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
101 test-data/empty_signalp3.tabular