Mercurial > repos > peterjc > tmhmm_and_signalp
comparison tools/protein_analysis/README @ 10:09ff180d1615 draft
Uploaded v0.1.3 with missing HMM file for RXLR tool included.
| author | peterjc |
|---|---|
| date | Wed, 27 Mar 2013 11:21:05 -0400 |
| parents | e52220a9ddad |
| children | 99b82a2b1272 |
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| 9:e52220a9ddad | 10:09ff180d1615 |
|---|---|
| 127 v0.1.0 - Added Promoter 2.0 wrapper (similar to SignalP & TMHMM wrappers) | 127 v0.1.0 - Added Promoter 2.0 wrapper (similar to SignalP & TMHMM wrappers) |
| 128 - Support Galaxy's <parallelism> tag for SignalP, TMHMM & Promoter | 128 - 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 | 129 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 | 130 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) | 131 - 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 | |
| 132 | 133 |
| 133 | 134 |
| 134 Developers | 135 Developers |
| 135 ========== | 136 ========== |
| 136 | 137 |
| 141 http://bitbucket.org/peterjc/galaxy-central/src/seq_analysis | 142 http://bitbucket.org/peterjc/galaxy-central/src/seq_analysis |
| 142 | 143 |
| 143 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use | 144 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use |
| 144 the following command from the Galaxy root folder: | 145 the following command from the Galaxy root folder: |
| 145 | 146 |
| 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 | 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 |
| 147 | 148 |
| 148 Check this worked: | 149 Check this worked: |
| 149 | 150 |
| 150 $ tar -tzf tmhmm_signalp_etc.tar.gz | 151 $ tar -tzf tmhmm_signalp_etc.tar.gz |
| 151 tools/protein_analysis/LICENSE | 152 tools/protein_analysis/LICENSE |
| 160 tools/protein_analysis/promoter2.py | 161 tools/protein_analysis/promoter2.py |
| 161 tools/protein_analysis/wolf_psort.xml | 162 tools/protein_analysis/wolf_psort.xml |
| 162 tools/protein_analysis/wolf_psort.py | 163 tools/protein_analysis/wolf_psort.py |
| 163 tools/protein_analysis/rxlr_motifs.xml | 164 tools/protein_analysis/rxlr_motifs.xml |
| 164 tools/protein_analysis/rxrl_motifs.py | 165 tools/protein_analysis/rxrl_motifs.py |
| 166 tools/protein_analysis/whisson_et_al_rxlr_eer_cropped.hmm | |
| 165 test-data/four_human_proteins.fasta | 167 test-data/four_human_proteins.fasta |
| 166 test-data/four_human_proteins.signalp3.tabular | 168 test-data/four_human_proteins.signalp3.tabular |
| 167 test-data/four_human_proteins.tmhmm2.tabular | 169 test-data/four_human_proteins.tmhmm2.tabular |
| 168 test-data/empty.fasta | 170 test-data/empty.fasta |
| 169 test-data/empty_tmhmm2.tabular | 171 test-data/empty_tmhmm2.tabular |