comparison tools/protein_analysis/README @ 1:3ff1dcbb9440

Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
author peterjc
date Tue, 07 Jun 2011 18:04:05 -0400
parents bca9bc7fdaef
children 6901298ac16c
comparison
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0:bca9bc7fdaef 1:3ff1dcbb9440
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