Mercurial > repos > peterjc > tmhmm_and_signalp

comparison tools/protein_analysis/README @ 13:dc958c2a963a draft

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Uploaded v0.2.2, adds missing test files
author peterjc
date Tue, 23 Apr 2013 12:47:49 -0400
parents 99b82a2b1272
children 6365217cd3de
comparison
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12:6753a9261390 13:dc958c2a963a
16 16
17 These wrappers are copyright 2010-2013 by Peter Cock, James Hutton Institute 17 These wrappers are copyright 2010-2013 by Peter Cock, James Hutton Institute
18 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. 18 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
19 Contributions/revisions copyright 2011 Konrad Paszkiewicz. All rights reserved. 19 Contributions/revisions copyright 2011 Konrad Paszkiewicz. All rights reserved.
20 See the included LICENCE file for details (an MIT style open source licence). 20 See the included LICENCE file for details (an MIT style open source licence).
21
21 22
22 Requirements 23 Requirements
23 ============ 24 ============
24 25
25 First install those command line tools you wish to use the wrappers for: 26 First install those command line tools you wish to use the wrappers for:
42 but put it on the path under the name hmmsearch2 (allowing it to co-exist 43 but put it on the path under the name hmmsearch2 (allowing it to co-exist
43 with HMMER 3), or edit rlxr_motif.py accordingly. 44 with HMMER 3), or edit rlxr_motif.py accordingly.
44 45
45 Verify each of the tools is installed and working from the command line 46 Verify each of the tools is installed and working from the command line
46 (when logged in as the Galaxy user if appropriate). 47 (when logged in as the Galaxy user if appropriate).
48
47 49
48 Manual Installation 50 Manual Installation
49 =================== 51 ===================
50 52
51 1. Create a folder tools/protein_analysis under your Galaxy installation. 53 1. Create a folder tools/protein_analysis under your Galaxy installation.
91 <tool file="protein_analysis/promoter2.xml" /> 93 <tool file="protein_analysis/promoter2.xml" />
92 </section> 94 </section>
93 95
94 Leave out the lines for any tools you do not wish to use in Galaxy. 96 Leave out the lines for any tools you do not wish to use in Galaxy.
95 97
96 4. Copy/move the following test files (from these archive) to Galaxy 98 4. Copy/move the test-data files (from this archive) to Galaxy's
97 subfolder test-data: 99 subfolder test-data.
98
99 four_human_proteins.fasta
100 four_human_proteins_signalp3.tabular
101 four_human_proteins_tmhmm2.tabular
102 empty.fasta
103 empty_tmhmm2.tabular
104 empty_signalp3.tabular
105 k12_ten_proteins.fasta
106 k12_ten_proteins_psortb_p_terse.tabular
107 100
108 5. Run the Galaxy functional tests for these new wrappers with: 101 5. Run the Galaxy functional tests for these new wrappers with:
109 102
110 ./run_functional_tests.sh -id tmhmm2 103 ./run_functional_tests.sh -id tmhmm2
111 ./run_functional_tests.sh -id signalp3 104 ./run_functional_tests.sh -id signalp3
143 v0.1.2 - Use the new <stdio> settings in the XML wrappers to catch errors 136 v0.1.2 - Use the new <stdio> settings in the XML wrappers to catch errors
144 - Use SGE style $NSLOTS for thread count (otherwise default to 4) 137 - Use SGE style $NSLOTS for thread count (otherwise default to 4)
145 v0.1.3 - Added missing file whisson_et_al_rxlr_eer_cropped.hmm to Tool Shed 138 v0.1.3 - Added missing file whisson_et_al_rxlr_eer_cropped.hmm to Tool Shed
146 v0.2.0 - Added PSORTb wrapper to the suite, based on earlier work 139 v0.2.0 - Added PSORTb wrapper to the suite, based on earlier work
147 contributed by Konrad Paszkiewicz. 140 contributed by Konrad Paszkiewicz.
141 v0.2.1 - Use a script to create the Tool Shed tar-ball (removed some stray
142 files accidentally included previously via a wildcard).
143 v0.2.2 - Include missing test files.
148 144
149 145
150 Developers 146 Developers
151 ========== 147 ==========
152 148
157 http://bitbucket.org/peterjc/galaxy-central/src/seq_analysis 153 http://bitbucket.org/peterjc/galaxy-central/src/seq_analysis
158 154
159 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use 155 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use
160 the following command from the Galaxy root folder: 156 the following command from the Galaxy root folder:
161 157
162 tar -czf ~/tmhmm_signalp_etc.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 tools/protein_analysis/promoter2.xml tools/protein_analysis/promoter2.py tools/protein_analysis/psortb.xml tools/protein_analysis/psortb.py tools/protein_analysis/wolf_psort.xml tools/protein_analysis/wolf_psort.py tools/protein_analysis/rxlr_motifs.xml tools/protein_analysis/rxlr_motifs.py tools/protein_analysis/whisson_et_al_rxlr_eer_cropped.hmm test-data/four_human_proteins.* test-data/empty.fasta test-data/empty_tmhmm2.tabular test-data/empty_signalp3.tabular test-data/k12_ten_proteins.fasta test-data/k12_ten_proteins_psortb_p_terse.tabular 158 $ ./tools/protein_analysis/make_tmhmm_and_signalp.sh
163 159
164 Check this worked: 160 This simplifies ensuring a consistent set of files is bundled each time,
165 161 including all the relevant test files.
166 $ tar -tzf ~/tmhmm_signalp_etc.tar.gz
167 tools/protein_analysis/LICENSE
168 tools/protein_analysis/README
169 tools/protein_analysis/suite_config.xml
170 tools/protein_analysis/seq_analysis_utils.py
171 tools/protein_analysis/signalp3.xml
172 tools/protein_analysis/signalp3.py
173 tools/protein_analysis/tmhmm2.xml
174 tools/protein_analysis/tmhmm2.py
175 tools/protein_analysis/promoter2.xml
176 tools/protein_analysis/promoter2.py
177 tools/protein_analysis/psortb.xml
178 tools/protein_analysis/psortb.py
179 tools/protein_analysis/wolf_psort.xml
180 tools/protein_analysis/wolf_psort.py
181 tools/protein_analysis/rxlr_motifs.xml
182 tools/protein_analysis/rxrl_motifs.py
183 tools/protein_analysis/whisson_et_al_rxlr_eer_cropped.hmm
184 test-data/four_human_proteins.fasta
185 test-data/four_human_proteins.signalp3.tabular
186 test-data/four_human_proteins.tmhmm2.tabular
187 test-data/empty.fasta
188 test-data/empty_tmhmm2.tabular
189 test-data/empty_signalp3.tabular
190 test-data/k12_ten_proteins.fasta
191 test-data/k12_ten_proteins_psortb_p_terse.tabular