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comparison tools/protein_analysis/README @ 8:391a142c1e60 draft

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author peterjc
date Tue, 26 Mar 2013 14:27:44 -0400
parents 5e62aefb2918
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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 2010-2012 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.
17 See the included LICENCE file for details (an MIT style open source licence). 19 See the included LICENCE file for details (an MIT style open source licence).
18 20
58 signalp3.py (Python wrapper script) 60 signalp3.py (Python wrapper script)
59 61
60 promoter2.xml (Galaxy tool definition) 62 promoter2.xml (Galaxy tool definition)
61 promoter2.py (Python wrapper script) 63 promoter2.py (Python wrapper script)
62 64
65 psortb.xml (Galaxy tool definition)
66 psortb.py (Python wrapper script)
67
63 wolf_psort.xml (Galaxy tool definition) 68 wolf_psort.xml (Galaxy tool definition)
64 wolf_psort.py (Python wrapper script) 69 wolf_psort.py (Python wrapper script)
65 70
66 rxlr_motifs.xml (Galaxy tool definition) 71 rxlr_motifs.xml (Galaxy tool definition)
67 rxlr_motifs.py (Python script) 72 rxlr_motifs.py (Python script)
75 by adding: 80 by adding:
76 81
77 <section name="Protein sequence analysis" id="protein_analysis"> 82 <section name="Protein sequence analysis" id="protein_analysis">
78 <tool file="protein_analysis/tmhmm2.xml" /> 83 <tool file="protein_analysis/tmhmm2.xml" />
79 <tool file="protein_analysis/signalp3.xml" /> 84 <tool file="protein_analysis/signalp3.xml" />
85 <tool file="protein_analysis/psortb.xml" />
80 <tool file="protein_analysis/wolf_psort.xml" /> 86 <tool file="protein_analysis/wolf_psort.xml" />
81 <tool file="protein_analysis/rxlr_motifs.xml" /> 87 <tool file="protein_analysis/rxlr_motifs.xml" />
82 </section> 88 </section>
83 <section name="Nucleotide sequence analysis" id="nucleotide_analysis"> 89 <section name="Nucleotide sequence analysis" id="nucleotide_analysis">
84 <tool file="protein_analysis/promoter2.xml" /> 90 <tool file="protein_analysis/promoter2.xml" />
93 four_human_proteins_signalp3.tabular 99 four_human_proteins_signalp3.tabular
94 four_human_proteins_tmhmm2.tabular 100 four_human_proteins_tmhmm2.tabular
95 empty.fasta 101 empty.fasta
96 empty_tmhmm2.tabular 102 empty_tmhmm2.tabular
97 empty_signalp3.tabular 103 empty_signalp3.tabular
104 k12_ten_proteins.fasta
105 k12_ten_proteins_psortb_p_terse.tabular
98 106
99 5. Run the Galaxy functional tests for these new wrappers with: 107 5. Run the Galaxy functional tests for these new wrappers with:
100 108
101 ./run_functional_tests.sh -id tmhmm2 109 ./run_functional_tests.sh -id tmhmm2
102 ./run_functional_tests.sh -id signalp3 110 ./run_functional_tests.sh -id signalp3
111 ./run_functional_tests.sh -id Psortb
112 ./run_functional_tests.sh -id rxlr_motifs
103 113
104 Alternatively, this should work (assuming you left the name and id as shown in 114 Alternatively, this should work (assuming you left the name and id as shown in
105 the XML file tool_conf.xml.sample): 115 the XML file tool_conf.xml.sample):
106 116
107 ./run_functional_tests.sh -sid Protein_sequence_analysis-protein_analysis 117 ./run_functional_tests.sh -sid Protein_sequence_analysis-protein_analysis
118
119 To check the section ID expected, use ./run_functional_tests.sh -list
108 120
109 6. Restart Galaxy and check the new tools are shown and work. 121 6. Restart Galaxy and check the new tools are shown and work.
110 122
111 123
112 History 124 History
127 v0.1.0 - Added Promoter 2.0 wrapper (similar to SignalP & TMHMM wrappers) 139 v0.1.0 - Added Promoter 2.0 wrapper (similar to SignalP & TMHMM wrappers)
128 - Support Galaxy's <parallelism> tag for SignalP, TMHMM & Promoter 140 - 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 141 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 142 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) 143 - Use SGE style $NSLOTS for thread count (otherwise default to 4)
144 v0.2.0 - Added PSORTb wrapper to the suite, based on earlier work
145 contributed by Konrad Paszkiewicz.
132 146
133 147
134 Developers 148 Developers
135 ========== 149 ==========
136 150
141 http://bitbucket.org/peterjc/galaxy-central/src/seq_analysis 155 http://bitbucket.org/peterjc/galaxy-central/src/seq_analysis
142 156
143 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use 157 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use
144 the following command from the Galaxy root folder: 158 the following command from the Galaxy root folder:
145 159
146 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 test-data/four_human_proteins.* test-data/empty.fasta test-data/empty_tmhmm2.tabular test-data/empty_signalp3.tabular 160 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 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
147 161
148 Check this worked: 162 Check this worked:
149 163
150 $ tar -tzf tmhmm_signalp_etc.tar.gz 164 $ tar -tzf ~/tmhmm_signalp_etc.tar.gz
151 tools/protein_analysis/LICENSE 165 tools/protein_analysis/LICENSE
152 tools/protein_analysis/README 166 tools/protein_analysis/README
153 tools/protein_analysis/suite_config.xml 167 tools/protein_analysis/suite_config.xml
154 tools/protein_analysis/seq_analysis_utils.py 168 tools/protein_analysis/seq_analysis_utils.py
155 tools/protein_analysis/signalp3.xml 169 tools/protein_analysis/signalp3.xml
156 tools/protein_analysis/signalp3.py 170 tools/protein_analysis/signalp3.py
157 tools/protein_analysis/tmhmm2.xml 171 tools/protein_analysis/tmhmm2.xml
158 tools/protein_analysis/tmhmm2.py 172 tools/protein_analysis/tmhmm2.py
159 tools/protein_analysis/promoter2.xml 173 tools/protein_analysis/promoter2.xml
160 tools/protein_analysis/promoter2.py 174 tools/protein_analysis/promoter2.py
175 tools/protein_analysis/psortb.xml
176 tools/protein_analysis/psortb.py
161 tools/protein_analysis/wolf_psort.xml 177 tools/protein_analysis/wolf_psort.xml
162 tools/protein_analysis/wolf_psort.py 178 tools/protein_analysis/wolf_psort.py
163 tools/protein_analysis/rxlr_motifs.xml 179 tools/protein_analysis/rxlr_motifs.xml
164 tools/protein_analysis/rxrl_motifs.py 180 tools/protein_analysis/rxrl_motifs.py
165 test-data/four_human_proteins.fasta 181 test-data/four_human_proteins.fasta
166 test-data/four_human_proteins.signalp3.tabular 182 test-data/four_human_proteins.signalp3.tabular
167 test-data/four_human_proteins.tmhmm2.tabular 183 test-data/four_human_proteins.tmhmm2.tabular
168 test-data/empty.fasta 184 test-data/empty.fasta
169 test-data/empty_tmhmm2.tabular 185 test-data/empty_tmhmm2.tabular
170 test-data/empty_signalp3.tabular 186 test-data/empty_signalp3.tabular
187 test-data/k12_ten_proteins.fasta
188 test-data/k12_ten_proteins_psortb_p_terse.tabular