comparison tools/protein_analysis/README @ 0:bca9bc7fdaef

Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
author peterjc
date Tue, 07 Jun 2011 18:03:34 -0400
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children 3ff1dcbb9440
comparison
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-1:000000000000 0:bca9bc7fdaef
1 This package contains Galaxy wrappers for two standalone command line protein
2 analysis tools (SignalP 3.0 and THMHMM 2.0) from the Center for Biological
3 Sequence Analysis at the Technical University of Denmark,
4 http://www.cbs.dtu.dk/cbs/
5
6 To use these Galaxy wrappers you must first install the CBS command line
7 tools. At the time of writing both SignalP 3.0 and TMHMM 2.0 are free for
8 academic use.
9
10 These wrappers are copyright 2010 by Peter Cock, SCRI, UK. All rights
11 reserved. See the included LICENCE file for details.
12
13 Installation
14 ============
15
16 1. Install the command line version of SignalP 3.0 and ensure it is on the
17 PATH, see: http://www.cbs.dtu.dk/services/SignalP/
18
19 2. Install the command line version of TMHMM 2.0 and ensure it is on the
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
26 tmhmm2.xml (Galaxy tool definition)
27 tmhmm2.py (Python wrapper script)
28 signalp3.xml (Galaxy tool definition)
29 signalp3.py (Python wrapper script)
30 seq_analysis_utils.py (shared Python code)
31 README (optional)
32
33 5. 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
35 by adding:
36
37 <section name="Protein sequence analysis" id="protein_analysis">
38 <tool file="protein_analysis/tmhmm2.xml" />
39 <tool file="protein_analysis/signalp3.xml" />
40 </section>
41
42 6. Copy/move the following test files (from these archive) to Galaxy
43 subfolder test-data:
44
45 four_human_proteins.fasta
46 four_human_proteins.signalp3.tsv
47 four_human_proteins.tmhmm2.tsv
48
49 7. Run the Galaxy functional tests for these new wrappers with:
50
51 ./run_functional_tests.sh -id tmhmm2
52 ./run_functional_tests.sh -id signalp3
53
54 Alternatively, this should work (assuming you left the name and id as shown in
55 the XML file tool_conf.xml.sample):
56
57 ./run_functional_tests.sh -sid Protein_sequence_analysis-protein_analysis
58
59 8. Restart Galaxy and check the new tools are shown and work.