Mercurial > repos > peterjc > tmhmm_and_signalp

annotate tools/protein_analysis/README @ 0:bca9bc7fdaef

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
parents
children 3ff1dcbb9440
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
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
46 four_human_proteins.signalp3.tsv
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
47 four_human_proteins.tmhmm2.tsv
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
48
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
49 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
50
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
51 ./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
52 ./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
53
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
54 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
55 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
56
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
57 ./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
58
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
59 8. Restart Galaxy and check the new tools are shown and work.