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comparison tools/protein_analysis/README @ 11:99b82a2b1272 draft

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Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz)
author peterjc
date Wed, 03 Apr 2013 10:49:10 -0400
parents 09ff180d1615
children dc958c2a963a
comparison
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10:09ff180d1615 11:99b82a2b1272
5 Sequence Analysis at the Technical University of Denmark, 5 Sequence Analysis at the Technical University of Denmark,
6 http://www.cbs.dtu.dk/cbs/ 6 http://www.cbs.dtu.dk/cbs/
7 7
8 * WoLF PSORT v0.2 from http://wolfpsort.org/ 8 * WoLF PSORT v0.2 from http://wolfpsort.org/
9 9
10 * PSORTb v3 from http://www.psort.org/downloads/index.html
11
10 Also, the RXLR motif tool uses SignalP 3.0 and HMMER 2.3.2 internally. 12 Also, the RXLR motif tool uses SignalP 3.0 and HMMER 2.3.2 internally.
11 13
12 To use these Galaxy wrappers you must first install the command line tools. 14 To use these Galaxy wrappers you must first install the command line tools.
13 At the time of writing they are all free for academic use. 15 At the time of writing they are all free for academic use, or open source.
14 16
15 These wrappers are copyright 2010-2012 by Peter Cock, James Hutton Institute 17 These wrappers are copyright 2010-2013 by Peter Cock, James Hutton Institute
16 (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.
17 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).
18 21
19 Requirements 22 Requirements
20 ============ 23 ============
21 24
58 signalp3.py (Python wrapper script) 61 signalp3.py (Python wrapper script)
59 62
60 promoter2.xml (Galaxy tool definition) 63 promoter2.xml (Galaxy tool definition)
61 promoter2.py (Python wrapper script) 64 promoter2.py (Python wrapper script)
62 65
66 psortb.xml (Galaxy tool definition)
67 psortb.py (Python wrapper script)
68
63 wolf_psort.xml (Galaxy tool definition) 69 wolf_psort.xml (Galaxy tool definition)
64 wolf_psort.py (Python wrapper script) 70 wolf_psort.py (Python wrapper script)
65 71
66 rxlr_motifs.xml (Galaxy tool definition) 72 rxlr_motifs.xml (Galaxy tool definition)
67 rxlr_motifs.py (Python script) 73 rxlr_motifs.py (Python script)
75 by adding: 81 by adding:
76 82
77 <section name="Protein sequence analysis" id="protein_analysis"> 83 <section name="Protein sequence analysis" id="protein_analysis">
78 <tool file="protein_analysis/tmhmm2.xml" /> 84 <tool file="protein_analysis/tmhmm2.xml" />
79 <tool file="protein_analysis/signalp3.xml" /> 85 <tool file="protein_analysis/signalp3.xml" />
86 <tool file="protein_analysis/psortb.xml" />
80 <tool file="protein_analysis/wolf_psort.xml" /> 87 <tool file="protein_analysis/wolf_psort.xml" />
81 <tool file="protein_analysis/rxlr_motifs.xml" /> 88 <tool file="protein_analysis/rxlr_motifs.xml" />
82 </section> 89 </section>
83 <section name="Nucleotide sequence analysis" id="nucleotide_analysis"> 90 <section name="Nucleotide sequence analysis" id="nucleotide_analysis">
84 <tool file="protein_analysis/promoter2.xml" /> 91 <tool file="protein_analysis/promoter2.xml" />
93 four_human_proteins_signalp3.tabular 100 four_human_proteins_signalp3.tabular
94 four_human_proteins_tmhmm2.tabular 101 four_human_proteins_tmhmm2.tabular
95 empty.fasta 102 empty.fasta
96 empty_tmhmm2.tabular 103 empty_tmhmm2.tabular
97 empty_signalp3.tabular 104 empty_signalp3.tabular
105 k12_ten_proteins.fasta
106 k12_ten_proteins_psortb_p_terse.tabular
98 107
99 5. Run the Galaxy functional tests for these new wrappers with: 108 5. Run the Galaxy functional tests for these new wrappers with:
100 109
101 ./run_functional_tests.sh -id tmhmm2 110 ./run_functional_tests.sh -id tmhmm2
102 ./run_functional_tests.sh -id signalp3 111 ./run_functional_tests.sh -id signalp3
112 ./run_functional_tests.sh -id Psortb
113 ./run_functional_tests.sh -id rxlr_motifs
103 114
104 Alternatively, this should work (assuming you left the name and id as shown in 115 Alternatively, this should work (assuming you left the name and id as shown in
105 the XML file tool_conf.xml.sample): 116 the XML file tool_conf.xml.sample):
106 117
107 ./run_functional_tests.sh -sid Protein_sequence_analysis-protein_analysis 118 ./run_functional_tests.sh -sid Protein_sequence_analysis-protein_analysis
119
120 To check the section ID expected, use ./run_functional_tests.sh -list
108 121
109 6. Restart Galaxy and check the new tools are shown and work. 122 6. Restart Galaxy and check the new tools are shown and work.
110 123
111 124
112 History 125 History
128 - Support Galaxy's <parallelism> tag for SignalP, TMHMM & Promoter 141 - Support Galaxy's <parallelism> tag for SignalP, TMHMM & Promoter
129 v0.1.1 - Fixed an error in the header of the tabular output from Promoter 142 v0.1.1 - Fixed an error in the header of the tabular output from Promoter
130 v0.1.2 - Use the new <stdio> settings in the XML wrappers to catch errors 143 v0.1.2 - Use the new <stdio> settings in the XML wrappers to catch errors
131 - Use SGE style $NSLOTS for thread count (otherwise default to 4) 144 - Use SGE style $NSLOTS for thread count (otherwise default to 4)
132 v0.1.3 - Added missing file whisson_et_al_rxlr_eer_cropped.hmm to Tool Shed 145 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
147 contributed by Konrad Paszkiewicz.
133 148
134 149
135 Developers 150 Developers
136 ========== 151 ==========
137 152
142 http://bitbucket.org/peterjc/galaxy-central/src/seq_analysis 157 http://bitbucket.org/peterjc/galaxy-central/src/seq_analysis
143 158
144 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use 159 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use
145 the following command from the Galaxy root folder: 160 the following command from the Galaxy root folder:
146 161
147 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/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 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
148 163
149 Check this worked: 164 Check this worked:
150 165
151 $ tar -tzf tmhmm_signalp_etc.tar.gz 166 $ tar -tzf ~/tmhmm_signalp_etc.tar.gz
152 tools/protein_analysis/LICENSE 167 tools/protein_analysis/LICENSE
153 tools/protein_analysis/README 168 tools/protein_analysis/README
154 tools/protein_analysis/suite_config.xml 169 tools/protein_analysis/suite_config.xml
155 tools/protein_analysis/seq_analysis_utils.py 170 tools/protein_analysis/seq_analysis_utils.py
156 tools/protein_analysis/signalp3.xml 171 tools/protein_analysis/signalp3.xml
157 tools/protein_analysis/signalp3.py 172 tools/protein_analysis/signalp3.py
158 tools/protein_analysis/tmhmm2.xml 173 tools/protein_analysis/tmhmm2.xml
159 tools/protein_analysis/tmhmm2.py 174 tools/protein_analysis/tmhmm2.py
160 tools/protein_analysis/promoter2.xml 175 tools/protein_analysis/promoter2.xml
161 tools/protein_analysis/promoter2.py 176 tools/protein_analysis/promoter2.py
177 tools/protein_analysis/psortb.xml
178 tools/protein_analysis/psortb.py
162 tools/protein_analysis/wolf_psort.xml 179 tools/protein_analysis/wolf_psort.xml
163 tools/protein_analysis/wolf_psort.py 180 tools/protein_analysis/wolf_psort.py
164 tools/protein_analysis/rxlr_motifs.xml 181 tools/protein_analysis/rxlr_motifs.xml
165 tools/protein_analysis/rxrl_motifs.py 182 tools/protein_analysis/rxrl_motifs.py
166 tools/protein_analysis/whisson_et_al_rxlr_eer_cropped.hmm 183 tools/protein_analysis/whisson_et_al_rxlr_eer_cropped.hmm
168 test-data/four_human_proteins.signalp3.tabular 185 test-data/four_human_proteins.signalp3.tabular
169 test-data/four_human_proteins.tmhmm2.tabular 186 test-data/four_human_proteins.tmhmm2.tabular
170 test-data/empty.fasta 187 test-data/empty.fasta
171 test-data/empty_tmhmm2.tabular 188 test-data/empty_tmhmm2.tabular
172 test-data/empty_signalp3.tabular 189 test-data/empty_signalp3.tabular
190 test-data/k12_ten_proteins.fasta
191 test-data/k12_ten_proteins_psortb_p_terse.tabular