Mercurial > repos > peterjc > tmhmm_and_signalp
comparison tools/protein_analysis/README @ 1:9a8a7f680dd6
Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
| author | peterjc |
|---|---|
| date | Tue, 07 Jun 2011 17:38:05 -0400 |
| parents | a2eeeaa6f75e |
| children | 747cec3192d3 |
comparison
equal
deleted
inserted
replaced
| 0:a2eeeaa6f75e | 1:9a8a7f680dd6 |
|---|---|
| 41 | 41 |
| 42 6. Copy/move the following test files (from these archive) to Galaxy | 42 6. Copy/move the following test files (from these archive) to Galaxy |
| 43 subfolder test-data: | 43 subfolder test-data: |
| 44 | 44 |
| 45 four_human_proteins.fasta | 45 four_human_proteins.fasta |
| 46 four_human_proteins.signalp3.tsv | 46 four_human_proteins_signalp3.tabular |
| 47 four_human_proteins.tmhmm2.tsv | 47 four_human_proteins_tmhmm2.tabular |
| 48 empty.fasta | |
| 49 empty_tmhmm2.tabular | |
| 50 empty_signalp3.tabular | |
| 48 | 51 |
| 49 7. Run the Galaxy functional tests for these new wrappers with: | 52 7. Run the Galaxy functional tests for these new wrappers with: |
| 50 | 53 |
| 51 ./run_functional_tests.sh -id tmhmm2 | 54 ./run_functional_tests.sh -id tmhmm2 |
| 52 ./run_functional_tests.sh -id signalp3 | 55 ./run_functional_tests.sh -id signalp3 |
| 55 the XML file tool_conf.xml.sample): | 58 the XML file tool_conf.xml.sample): |
| 56 | 59 |
| 57 ./run_functional_tests.sh -sid Protein_sequence_analysis-protein_analysis | 60 ./run_functional_tests.sh -sid Protein_sequence_analysis-protein_analysis |
| 58 | 61 |
| 59 8. Restart Galaxy and check the new tools are shown and work. | 62 8. Restart Galaxy and check the new tools are shown and work. |
| 63 | |
| 64 | |
| 65 History | |
| 66 ======= | |
| 67 | |
| 68 v0.0.1 - Initial release | |
| 69 v0.0.2 - Corrected some typos in the help text | |
| 70 - Renamed test output file to use Galaxy convention of *.tabular | |
| 71 v0.0.3 - Check for tmhmm2 silent failures (no output) | |
| 72 - Additional unit tests | |
| 73 | |
| 74 Developers | |
| 75 ========== | |
| 76 | |
| 77 These wrappers are currently being developed on the following hg branch: | |
| 78 http://bitbucket.org/peterjc/galaxy-central/src/seq_analysis | |
| 79 | |
| 80 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use | |
| 81 the following command from the Galaxy root folder: | |
| 82 | |
| 83 tar -czf tmhmm_and_signalp.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 test-data/four_human_proteins.* test-data/empty.fasta test-data/empty_tmhmm2.tabular test-data/empty_signalp3.tabular | |
| 84 | |
| 85 Check this worked: | |
| 86 | |
| 87 $ tar -tzf tmhmm_and_signalp.tar.gz | |
| 88 tools/protein_analysis/LICENSE | |
| 89 tools/protein_analysis/README | |
| 90 tools/protein_analysis/suite_config.xml | |
| 91 tools/protein_analysis/seq_analysis_utils.py | |
| 92 tools/protein_analysis/signalp3.xml | |
| 93 tools/protein_analysis/signalp3.py | |
| 94 tools/protein_analysis/tmhmm2.xml | |
| 95 tools/protein_analysis/tmhmm2.py | |
| 96 test-data/four_human_proteins.fasta | |
| 97 test-data/four_human_proteins.signalp3.tabular | |
| 98 test-data/four_human_proteins.tmhmm2.tabular | |
| 99 test-data/empty.fasta | |
| 100 test-data/empty_tmhmm2.tabular | |
| 101 test-data/empty_signalp3.tabular |