| Previous changeset 2:88f002677c63 (2013-05-02) Next changeset 4:26ce6e046040 (2013-06-24) |
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Commit message:
Uploaded v0.0.5, automated Biopython installation |
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modified:
tools/filters/get_orfs_or_cdss.txt tools/filters/get_orfs_or_cdss.xml |
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added:
tools/filters/repository_dependencies.xml |
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removed:
test-data/Ssuis.fasta |
| b |
| diff -r 88f002677c63 -r 1ce1b6132012 test-data/Ssuis.fasta --- a/test-data/Ssuis.fasta Thu May 02 13:12:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,33460 +0,0 @@\n->Streptococcus_suis\n-ATGAACCAAGAACAACTTTTTTGGCAACGATTTATTGAATTGGCAAAGGTAAATTTTAAG\n-CCATCTATTTATGATTTTTATGTCGCTGATGCAAAATTACTCGGAATCAACCAGCAAGTT\n-GCCAATATTTTCTTAAATCGTCCATTTAAAAAAGATTTCTGGGAAAAAAACTTCGAAGAG\n-TTAATGATTGCCGCTAGTTTTGAAAGCTACGGAGAGCCTCTTACCATCCAATATCAATTT\n-ACAGAGGATGAACAGGAGATTAGGAATACTACAAACACAAGAAGTTCAATAGTTCACCAG\n-GTACAGACACTTGAGCCGGCTACTCCTCAAGAAACTTTTAAACCGGTTCATTCTGATATA\n-AAATCCCAGTACACCTTTGCTAATTTTGTACAAGGAGACAATAATCACTGGGCAAAGGCT\n-GCAGCTTTAGCTGTATCTGATAACCTAGGTGAGCTCTACAATCCATTATTCATTTTTGGT\n-GGTCCTGGTCTTGGAAAAACTCATATTTTAAATGCGATTGGAAATAAGGTTCTAGCCGAT\n-AATCCCCAGGCAAGGATAAAATATGTCTCATCGGAAACATTCATCAATGAATTTTTAGAA\n-CACCTCCGTCTCAATGATATGGAAAGTTTCAAAAAAACCTATCGCAATCTGGACTTACTT\n-CTAATTGATGACATTCAGTCTCTCCGTAATAAAGCAACAACACAGGAAGAATTTTTCCAT\n-ACTTTTAATGCGCTTCATGAAAAAAATAAGCAGATTGTACTCACAAGCGACCGTAATCCC\n-GATCACTTAGACAATTTGGAAGAAAGACTAGTAACACGTTTCAAATGGGGGTTAACCAGT\n-GAAATCACTCCACCTGATTTTGAAACACGTATCGCAATTTTACGTAACAAGTGCGAGAAC\n-CTGCCTTACAACTTTACAAATGAGACGCTATCCTATCTAGCTGGGCAATTTGATTCGAAC\n-GTACGTGACCTTGAAGGTGCCTTAAAAGATATCCATTTGATAGCCACTATGCGTCAACTG\n-TCTGAGATAAGTGTCGAGGTTGCTGCTGAGGCTATTCGATCAAGAAAACAAACAAATCCA\n-CAAAACATGGTTATTCCTATTGAGAAAATCCAAACCGAAGTGGGAAATTTCTACGGTGTC\n-AGCTTGAAAGAATTAAAAGGTTCTAAGCGTGTTCAACATATCGTTCACGCGCGACAAGTT\n-GCTATGTTTTTAGCACGTGAAATGACAGACAATTCCCTTCCAAAAATTGGGAAAGAATTT\n-GGTAATCGAGACCATACAACCGTTATGCATGCATACAATAAAATAAAAACTCTCCTCTTG\n-GATGATGAGAATTTAGAAATAGAGATTACCAGTATAAAAAATAAACTTCGTTAACCTGTG\n-TATAACTTTTTTAAAAAACTCTGTTTTTTCCACAAGTTGTGAACAAGTTAATTTCCGCAG\n-TTTTATTGGTCTTTCATCACTTTTCCACAGAATACACAGAGACTACTATTACTATTAACC\n-TTATAGATAATAAATAAAGGAGAATCCATGATTCAATTTTCTATTAATAAAAATATATTT\n-CTACAAGCACTTAGTATTACTAAACGGGCAATCAGTACAAAAAATGCTATTCCAATTCTT\n-TCAACAGTAAAAATTACAGTAACTAGTGAAGGAATCACTTTAACTGGTTCAAATGGACAA\n-ATCTCGATAGAACATTTTATTTCTATTCAAGATGAAAATGCAGGGCTTTTGATCAGTTCT\n-CCAGGTTCCATTCTCTTAGAAGCTGGTTTCTTTATTAATGTCGTATCCAGTATGCCGGAT\n-TTGGTCCTTGACTTCAATGAAATTGAACAAAAGCAAATCGTTTTGACAAGTGGTAAGTCT\n-GAAATCACATTAAAGGGAAAAGAAGCAGAACAGTATCCTCGTTTACAGGAAGTTCCAACT\n-TCAAAACCATTGGTGTTAGAAACCAAAGTATTAAAACAAACAATTAATGAAACAGCATTT\n-GCAGCTTCTACACAAGAAAGTCGTCCTATTCTTACGGGTGTTCATTTTGTTTTAACAGAA\n-AATAAAAATCTAAAAACTGTTGCAACAGATTCACACCGTATGAGCCAACGGAAATTGGTC\n-CTTGATACCTCTGGTGATGATTTTAATGTTGTCATTCCAAGTCGTTCTCTCCGTGAATTT\n-ACTGCAGTTTTTACAGATGATATTGAAACAGTAGAAGTCTTCTTTTCAAATAATCAAATC\n-CTTTTTAGAAGCGAGCATATTAGCTTCTATACACGCTTATTAGAAGGTACCTACCCTGAT\n-ACCGACCGCTTAATTCCAACTGAGTTTAAAACAACTGCAATTTTTGATACTGCAAATCTT\n-CGTCACTCGATGGAGCGTGCTCGTCTTCTTTCAAATGCAACCCAAAATGGTACAGTAAAA\n-CTAGAAATTGCTAATAATGTTGTATCGGCTCATGTAAATTCTCCAGAAGTTGGACGTGTG\n-AATGAGGAATTAGATACTGTAGAAGTATCAGGTGAAGATTTAGTAATCAGCTTTAACCCA\n-ACTTACTTGATAGAAGCATTGAAAGCCACAACTAGTGAACAAGTGAAAATTAGCTTTATC\n-TCTTCTGTCCGTCCATTTACATTGATTCCAAATAATGAAGGGGAAGATTTTATTCAATTG\n-GTTACACCAGTTCGTACCAACTAAATAATATTAAGAACGGCTAAACTAGCCGTTTTTATG\n-TTATACTAAAAAATAGCACCTAGCTTATTTTTATATATTTAGTGATGGGGAATAAATGAC\n-GTTATATATATTAGCTAATCCTAATGCTGGTAGCCATACTGCTGAACATATCATATTCAA\n-AATAAAAGAAAGTTATCCACAGCTTGCAGTTAACATTTTTATGACAGTTGGTCCTGAGGA\n-TGAAAAAAGTCAAATAGAGGCTATTTTAAAGGAGTTTGTCAGTAGTGAAGATCAATTAAT\n-GATTTTAGGCGGAGACGGCACACTATCTAAAGCTTTGCGTTTTTGGCCAGCTAGTCTACC\n-GTTTGCTTATTATCCAACAGGATCTGGAAATGATTTTGCTAAGGCAATGAATATAACATC\n-GCTATATAGAAGTGTAGATGCCATTTTAGAGAGAAAAACAAGTCGGATATATGTTTTAAA\n-CAGTTCATACGGAACGGTTGTAAACAGTATGGATTTTGGCTTTGCAGCTCAAGTTATCAA\n-TGGTTCAACGAATTCAATTTTGAAAAAAATTCTGAACAAGGTAAAACTTGGGAAGTTAAC\n-TTATCTATTCTTTGGTATTAAAACATTATTTTCAAAACAAGCTATAAACTTAGAATTAAC\n-TCTTGATGAAAAATCTTATCAGTTAGATAATCTCTTTTTTATTTCTGTAGCAAATAGTCT\n-TTATTTTGGTGGAGGAATCATGATATGGCCAACAGCAAGTGCTAAAAAGAAGGAAGTAGA\n-TATTGTTTACTTCAAAAATGGAAATTTCTACCAACGTCTACAATCATTGTTAGCCTTATT\n-AACGAAGAGGCATGAATCTTCTCATACGATTCAGCATTTAACAGGGGTAGATGTAGTTTT\n-AAAATCAAAAGAAAAATTATTATTGCAAATAGATGGAGAGACATGCACTGCAAATGAGGT\n-AACGTTAACCTATCAGGAAAGAAGTATGTATCTTTAAGGAGGAAGTATGTACCAATTAGG\n-AACCTTTGTCGAAATGAAAAAGCCCCATGCCTGTGTCATCAAATCGACCGGAAAGAAGGC\n-TAATAAATGGGAGGTTATCCGTCTAGGAGCGGATATTAAAATCCGCTGTACCAACTGTGA\n-CCATGTCGTTATGATGAGCCGGCATGATTTTGAACGAAAAATGAAACAAGT'..b'CTCTACCAACTGAGCTA\n-TGGCGGAAGAAATAGTCCGTACGGGATTCGAACCCGTGTTACCGCCGTGAAAAGGCGGTG\n-TCTTAACCCCTTGACCAACGGACCATTTTTAGAACAATAACTAGTATAATACATGTGACT\n-TTGTTTGTCAATACATTTTTTGATTTTTTATTGTATTGACAGAGTGCTTTGTTTAATGTA\n-AAATAAAATGGTTAAGGTTCCATAGCTCAGCTGGATAGAGCATTCGCCTTCTAAGCGAAC\n-GGTCGCAGGTTCGAATCCTGCTGGAATCATTTAGACCTACCTCGAGTAGGTCTTTTTTCT\n-TGCCATAATTCATAATTAATATATAACACTGGCAAAATCAGACCAATAAGGGCATATTCT\n-TCAAATTGGAAGGATAGGTGAGTAGATATGATGACACCTAGCATAAACCCTATAATGGTC\n-AATAAGATGTTTCTACCTGTTTTTCTAAGTTCTGAATCTTTTTCAATAACTCCTTTAAAC\n-CAGAGATAAGCAGCATTTTTGACATTCCCTGTCATCATCACATTGGCATACGGAGCACCT\n-CGTAACCTTCTAAATGTTTCTACTTGAATAGAGGCTACGAAGGCTAGACTAGCAATTGTA\n-AAAGACGCAGGCATTATAGGTGAGAGAATGATAGTTAGTAAAATAAGAACTAACATCATT\n-ACACTACTACCAAAGTGCCAAGACCATGTTTGTTTTTCAAAATACCTTCTTGCTAAGTAG\n-GTAAAAAATTGTCCGAATACAAAAAATAAAATGGGAATGGAAAAATTAACTACCTGCGCA\n-AAATCACCTTTAGCTAAAAAATAAGCTAGGGAAATAACATTTCCAGATTGTACGCCAGCA\n-AAGCGACCACCCTGAGTCACAAAAGTAAAGGCATTTAAATAACCACTGATAAACGTTAAT\n-GAACAAGCAATTCTCAATCCCTCAAAAACACGATACTCTTTTTGATTCATTTTCACTCCT\n-TGTTTCACGTGAAACTACTTATGATATGGGCTTCCCTGCTGAATCATAAATGCACGATAA\n-ATCTGCTCGATGAGAACTAATTTCATTAGTTGATGGGGAAGTGTCAACTGTCCAAAACTC\n-ATCAACAAATTAGCTCTTTTTTTAATACAAGAATCGAGACCCAAACTACCACCGATGATA\n-AAAGTTATATCTGAATACCCATTTACTGCAATGTCAGATATCCTTTGACTAAATTCTTCC\n-GATGGAAATTGTTTCCCTTCTATCGCTAAGGCAATGACAAAATCTCGCTCTCCAATTTTA\n-GACATAATTCTATCGGCTTCTTTTTTTAATATTTGTTCATTCTCTGCCTGACTGGCTTTA\n-TCTGGTGTTTTTTCATCAGGAAGCTCAATCATATCCAACTTAGTAAATCGTCCCAATCGT\n-TTACTATATTCTGCAATACCTTCTTTGAGGTACTTTTCTTTCAATTTTCCAACGGTAATC\n-AATTTTATTTTCATAAAATAATTGTAACATATCCACAAGCATACGACAGAAAATATTTTT\n-AGAAAATCAGGATATGGCTACAGTTTTTCACATAATTCACAGAGTTATCCACAGGTTGTG\n-GATTGATTTTTGAAAACTTTAAGTTATAATTAAGAAAGAAATAGTACTCTTAAGGAAAAT\n-TAAAGAAATGGAAAGGATTCCTTATATGAAAAAATATTTGAAATTTGCGATTTTATTTGT\n-AATTGGATTTTTTGGGGGTCTTATCGGGGCCTTGTCAGCCTCTTTCTTCCAGCCACAGGT\n-GCAACAAGCAAATTCTGCTATCACTAGTGTCAGCAATGTTCAATATAATAATGAAACTTC\n-CACCACAAAAGCTGTAGAGAAAGTACAAAATGCTGTTGTGTCTGTTATTAATTACCAAAA\n-ATCAGCCAACAATAGTCTTGGTGTTATCTTTGGAAATATTGAATCATCTGACGAACTAGC\n-TGTTGCTGGAGAGGGGTCTGGGGTTATCTATAAAAAATATGGTCAATATGCCTATATTGT\n-GACAAATACGCATGTTATTAATAACGCAGAAAAGATTGATATCCTTTTAGCATCTGGAGA\n-AAAAATTAGCGGTGAACTTGTTGGTTCCGATACATATTCTGATATAGCTGTTATAAAAAT\n-ATCAGCAGATAAAGTCACTGCTGTTGCTGAATTTGCTGATTCCGATACAATTAAAGTTGG\n-AGAAACTGCTATCGCAATTGGTAGTCCTCTAGGTAGCGTCTACGCCAATACAGTTACCCA\n-GGGTATTATTTCTAGCTTAAGTCGGACAGTTACTTCACAATCAAAAGATGGACAAACAAT\n-CTCAACTAACGCTATTCAAACTGATACAGCTATCAACCCTGGAAACTCTGGCGGACCGTT\n-AATCAATACCCAAGGACAAGTGATAGGCATTACCTCTAGCAAAATTACCTCAAGTTCTGC\n-AAATAGCTCAGGCGTGGCTGTAGAAGGGTTGGGATTTGCTATTCCTGCAAATGATGCCGT\n-AGCTATTATCAATCAGCTTGAAAAAACTGGACAAGTTAGCCGACCTGCTCTTGGAGTTCA\n-TATGGTTAACTTGACGACCTTGTCAACTAGTCAATTAGAAAAAGCTGGATTATCAAATAC\n-GGAATTAACATCCGGTGTAGTAATTGTCTCTACACAAAGTGGGCTACCTGCAGATGGAAA\n-ATTAGAAACTTTTGATGTTATTACTGAGATTGACGGAGAAGCTATTCAAAATAAGAGTGA\n-CCTCCAGAGCGCTCTCTACAAACATCAAATTGGAGATACAATCACTGTAACTTATTACCG\n-CAATAATCAGAAACAAACTGTTGACATTAAGTTGACACATTCTACAGAAGAACTTAGCGA\n-ATAATTGACAAATGAGACTTTACACAATTGTAAAGTCTCATTTTTTTTGCTAGAATAAGG\n-ATATATGGAAGAATTACGTACACTAAATATTTCAGAAATCCATCCCAATCCCTATCAGCC\n-AAGAATTCATTTTGATGAAAAGGAGCTACTTGAGCTCGCTCAATCTATTAAGGAAAATGG\n-CTTAATTCAACCGATTATTGTAAGAAAATCTTCTATTATCGGATACGAATTATTAGCTGG\n-AGAAAGAAGGTTGCGAGCCAGTCAATTAGCTGGACTGACTACAATACCAGCAGTGGTAAA\n-AGAACTGACTGATGATGATTTACTCTATCAGGCTATCATAGAGAATCTGCAGCGTTCTAA\n-CTTAAATCCGATAGAAGAAGCAGCCTCTTATCAAAAATTGATTAGTAGAGGGTTAACACA\n-TGATGAAGTTGCTCAAATCATGGGAAAATCAAGACCATATATCAGTAATTTATTGCGCCT\n-ACTAAATCTATCATCTCAGACTAAACAAGCTGTAGAAGAAGGAAAAATTTCACAAGGGCA\n-CGCGCGACAATTGGTGTCATTTTCAGAAGAAAAGCAAGCCGAATGGGTTCAACTCATTTT\n-ATCAAAGGATTTAAGTGTGCGTACGCTTGAAAAATTAATAGCTGCAAATAAGAAAAAACA\n-CACTAAGCTTAAACAACGCGACCAATTTTTAAAAGAACAGGAAGATTCACTCAGTAAAAC\n-TCTTGGAACAGCTACAAAAATTATCAAGAAGAAAAACGGGAGCGGAGAAATTCGGATTAG\n-CTTTAATGACCTCGATGAATTCGAAAGAATTATCAACAATTTTAAATAGACTTGTTTACA\n-ATTTATTTTTATAAACACTCTTTTCCACACTAAAATCATTACAAAAAGTCAGGACCAGCA\n-AGGGTTCTGACTTTTATTCACATCTTGTGGAAAACTTTTCTTAACAGTGTGGATTTTAAA\n-AATTATCTGTGGAAAACTTTTGTTTTTTATGGTACACTATTCTAACGAATATAATGTGAA\n-AGGGGGAAAAT\n' 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| diff -r 88f002677c63 -r 1ce1b6132012 tools/filters/get_orfs_or_cdss.txt --- a/tools/filters/get_orfs_or_cdss.txt Thu May 02 13:12:15 2013 -0400 +++ b/tools/filters/get_orfs_or_cdss.txt Mon Jun 24 02:22:09 2013 -0400 |
| b |
| @@ -17,14 +17,15 @@ Automated Installation ====================== -This should be straightforward, Galaxy should automatically download and install -the tool from the Galaxy Tool Shed, and run the unit tests. +This should be straightforward using the Galaxy Tool Shed, which should be +able to automatically install the dependency on Biopython, and then install +this tool and run its unit tests. Manual Installation =================== -There are just two files to install: +There are just two files to install to use this tool from within Galaxy: * get_orfs_or_cdss.py (the Python script) * get_orfs_or_cdss.xml (the Galaxy tool definition) @@ -55,6 +56,7 @@ v0.0.3 - Include unit tests. - Record Python script version when run from Galaxy. v0.0.4 - Link to Tool Shed added to help text and this documentation. +v0.0.5 - Automated intallation of the Biopython dependency. Developers @@ -66,7 +68,7 @@ For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use the following command from the Galaxy root folder: -$ tar -czf get_orfs_or_cdss.tar.gz tools/filters/get_orfs_or_cdss.* test-data/get_orf_input*.fasta test-data/Ssuis.fasta +$ tar -czf get_orfs_or_cdss.tar.gz tools/filters/get_orfs_or_cdss.* tools/filters/repository_dependencies.xml test-data/get_orf_input*.fasta test-data/Ssuis.fasta Check this worked: @@ -74,6 +76,7 @@ filter/get_orfs_or_cdss.py filter/get_orfs_or_cdss.txt filter/get_orfs_or_cdss.xml +tools/filters/repository_dependencies.xml test-data/get_orf_input.fasta test-data/get_orf_input.Suis_ORF.nuc.fasta test-data/get_orf_input.Suis_ORF.prot.fasta |
| b |
| diff -r 88f002677c63 -r 1ce1b6132012 tools/filters/get_orfs_or_cdss.xml --- a/tools/filters/get_orfs_or_cdss.xml Thu May 02 13:12:15 2013 -0400 +++ b/tools/filters/get_orfs_or_cdss.xml Mon Jun 24 02:22:09 2013 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="get_orfs_or_cdss" name="Get open reading frames (ORFs) or coding sequences (CDSs)" version="0.0.4"> +<tool id="get_orfs_or_cdss" name="Get open reading frames (ORFs) or coding sequences (CDSs)" version="0.0.5"> <description>e.g. to get peptides from ESTs</description> <version_command interpreter="python">get_orfs_or_cdss.py --version</version_command> <command interpreter="python"> |
| b |
| diff -r 88f002677c63 -r 1ce1b6132012 tools/filters/repository_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/filters/repository_dependencies.xml Mon Jun 24 02:22:09 2013 -0400 |
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| @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<repositories description="This requires Biopython as a dependency."> +<!-- Leave out the tool shed and revision to get the current + tool shed and latest revision at the time of upload --> +<repository changeset_revision="627c7b41b970" name="package_biopython_1_61" owner="biopython" toolshed="http://testtoolshed.g2.bx.psu.edu" /> +</repositories> |