Mercurial > repos > peterjc > tmhmm_and_signalp
comparison tools/protein_analysis/README @ 9:9a9971a1e55e draft
Uploaded v0.2.0a
(As before but adding missing RXLR HMM file)
| author | peterjc |
|---|---|
| date | Wed, 27 Mar 2013 11:15:44 -0400 |
| parents | 391a142c1e60 |
| children | 7c1eda453701 |
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| 8:391a142c1e60 | 9:9a9971a1e55e |
|---|---|
| 139 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) |
| 140 - Support Galaxy's <parallelism> tag for SignalP, TMHMM & Promoter | 140 - Support Galaxy's <parallelism> tag for SignalP, TMHMM & Promoter |
| 141 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 |
| 142 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 |
| 143 - Use SGE style $NSLOTS for thread count (otherwise default to 4) | 143 - Use SGE style $NSLOTS for thread count (otherwise default to 4) |
| 144 v0.1.3 - Added missing file whisson_et_al_rxlr_eer_cropped.hmm to Tool Shed | |
| 144 v0.2.0 - Added PSORTb wrapper to the suite, based on earlier work | 145 v0.2.0 - Added PSORTb wrapper to the suite, based on earlier work |
| 145 contributed by Konrad Paszkiewicz. | 146 contributed by Konrad Paszkiewicz. |
| 146 | 147 |
| 147 | 148 |
| 148 Developers | 149 Developers |
| 155 http://bitbucket.org/peterjc/galaxy-central/src/seq_analysis | 156 http://bitbucket.org/peterjc/galaxy-central/src/seq_analysis |
| 156 | 157 |
| 157 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use | 158 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use |
| 158 the following command from the Galaxy root folder: | 159 the following command from the Galaxy root folder: |
| 159 | 160 |
| 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 | 161 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 |
| 161 | 162 |
| 162 Check this worked: | 163 Check this worked: |
| 163 | 164 |
| 164 $ tar -tzf ~/tmhmm_signalp_etc.tar.gz | 165 $ tar -tzf ~/tmhmm_signalp_etc.tar.gz |
| 165 tools/protein_analysis/LICENSE | 166 tools/protein_analysis/LICENSE |
| 176 tools/protein_analysis/psortb.py | 177 tools/protein_analysis/psortb.py |
| 177 tools/protein_analysis/wolf_psort.xml | 178 tools/protein_analysis/wolf_psort.xml |
| 178 tools/protein_analysis/wolf_psort.py | 179 tools/protein_analysis/wolf_psort.py |
| 179 tools/protein_analysis/rxlr_motifs.xml | 180 tools/protein_analysis/rxlr_motifs.xml |
| 180 tools/protein_analysis/rxrl_motifs.py | 181 tools/protein_analysis/rxrl_motifs.py |
| 182 tools/protein_analysis/whisson_et_al_rxlr_eer_cropped.hmm | |
| 181 test-data/four_human_proteins.fasta | 183 test-data/four_human_proteins.fasta |
| 182 test-data/four_human_proteins.signalp3.tabular | 184 test-data/four_human_proteins.signalp3.tabular |
| 183 test-data/four_human_proteins.tmhmm2.tabular | 185 test-data/four_human_proteins.tmhmm2.tabular |
| 184 test-data/empty.fasta | 186 test-data/empty.fasta |
| 185 test-data/empty_tmhmm2.tabular | 187 test-data/empty_tmhmm2.tabular |