Mercurial > repos > peterjc > clc_assembly_cell
changeset 3:93ef6468b288 draft
Uploaded v0.0.2 which uses the described environment variable to find the binaries
author | peterjc |
---|---|
date | Fri, 21 Nov 2014 06:40:45 -0500 |
parents | 6e145e4715a7 |
children | 95a5f56a24eb |
files | test-data/NC_010642.fna tools/clc_assembly_cell/README.rst tools/clc_assembly_cell/clc_assembler.xml tools/clc_assembly_cell/clc_mapper.xml tools/clc_assembly_cell/repository_dependencies.xml tools/clc_assembly_cell/tool_dependencies.xml |
diffstat | 6 files changed, 298 insertions(+), 50 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NC_010642.fna Fri Nov 21 06:40:45 2014 -0500 @@ -0,0 +1,245 @@ +>gi|187250362|ref|NC_010642.1| Panthera tigris mitochondrion, complete genome +GGGTTAATGACTAATCAGCCCATGATCACACATAACTGTGGTGTCATGCATTTGGTATTTTTAATTTTTA +GGGGGTCGAACTTGCTATGACTCAGCTATGACCTAAAGGTCCCGACTCAGTCAAATATAATGTAGCTGGA +CTTATTCTCTATGCGGGGGTTCCACACGTACAACAAACAAGGTGTTATTCAGTCAATGGTCACAGGACAT +ATACTTAAATTCCTATTGTTCCACAGGACACGGCATGCGCGCACCCACGTATACGCGTACACGTATACAC +GTATACACGTACACACGTACACACGTACACACGTACACACGTACACACGTATACACGTATACACGTATAC +ACGTATACACGTATACACGTATACACGTATACACGTATACACGTATACACGTATACACGTACACACGTAC +ACACGTACACACGTACACACGTATACACGTATACACGTATACACGTATACACGTATACGCGTACACGTAC +ACACGTACACACGTACACACGTACACACGTACACACGTACACACGTACACACGTACACACGTACACACGT +ACACACGTACACACGTACACACGTACACACGTACACACGTATACACGTATACACGTATACACGTATACAC +ATGCAAACTTTTTTGATTTAGTAAATAATTAGCTTAACCAAACCCCCCTTACCCCCCGTTAATCTTATTT +ATTATAGTACGTGTTTATTTCTGTCTTGCCAAACCCCAAAAACAAGACTAAACCCGTATCTAGGCACAAG +GCCTAAGATTAACGTTTACAAACTCTACCAACCCCATCATTACCAATTATTAATACTAAATCATAACTTC +GTTCGCAGTTATCTATAGATACGACAACCCGATCTCTAATTCGTCCCTATCGAACAATATTTACATACCC +AACAACCCTATGTCTTGGTTAATGTAGCTTAAATATATTAAAGCAAGGCACTGAAAATGCCTAGATGGGC +CGCCAGGCTCCATAAACATAAAGGTTTGGTCCTAGCCTTTCCATTAGTTGTTAATAAAATTACACATGCA +AGCCTCCGCATCCCGGTGAAAATGCCCTCTAAATCACCCAGTGATCCAAAGGAGCCGGTATCAAGTACAC +AACCATTGTAGCTCATGACACCTTGCTCAGCCACACCCCCACGGGACACAGCAGTGATAAAAATTAAGCC +ATGAATGAAAGTTCGACTAAGCTATATTAAATTAGGGTTGGTAAATTTCGTGCCAGCCACCGCGGTCATA +CGATTAACCCAAACTAATAGACCCACGGCGTAAAGCGTGTTACAGAAAAAAGTATACTAAAGTTAAGCCT +TAACTAGGCTGTAAAAAGCCACAGTTAACGTAAAAATACAGCACGAAAGTAACTTTAATATTTCTGACCA +CACGATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCCTAAACCTAGATAGTTAACC +CAAACAAAACTATCCGCCAGAGAACTACTAGCAACAGCTTAAAACTCAAAGGACTTGGCGGTGCTTTATA +TCCCTCTAGAGGAGCCTGTTCCATAATCGATAAACCCCGATAAACCTCACCATCTCTTGCTAATTCAGCC +TATATACCGCCATCTTCAGCAAACCCTAAAAAGGAAGAAAAGTAAGCACAAGTATCTTAACATAAAAAAG +TTAGGTCAAGGTGTAGCCCATGAGATGGGGAAGTAATGGGCTACATTTTCTATAACTAGAACATCCACGA +AAATCCTTATGAAATTAAGTATTAAAGGAGGATTTAGTAGTAAATTCGAGAATAGAGAGCTCGATTGAAT +CGGGCCATGAAGCACGCACACACCGCCCGTCACCCTCCTCAAGTGATTAGACCCCAAAGAAACCTATTCA +AACCACTACACCCACAAGAGGAGACAAGTCGTAACAAGGTAAGCATACTGGAAAGTGTGCTTGGATAACA +AGATGTAGCTTAAACAAAGCATCTGGCCTACACCCAGAAGATTTCATATTAAACTGACCATCTTGAGCTA +GAGCTAGCCCAACTACCCATAAACACAACTAACATTAGAAAGTAAAACAAAACATTTAGTTACTCTAAAA +AGTATAGGAGATAGAAATTTAACTCGGCGCTATAGAAAAAGTACCGCAAGGGAATGATGAAAGAAAAAAC +TAAAAGCACTATACAGCAAAGATTACCCCTTGTACCTTTTGCATAATGAATTAGCTAGAATAACCTAACA +AAGAGAACTTCAGCTAGGCCCCCCGAAACCAGACGAGCTACCCATAAACAATCTATTACAGGATGAACTC +GTCTATGTTGCAAAATAGTGAGAAGATTTATGGGTAGAGGTGAAAAGCCTAACGAGCCTGGTGATAGCTG +GTTGCCCAGAACAGAATCTTAGTTCAGCTTTAAACTTACCTCAAAAACCCTAAAATTCCAATGTAAGTTT +AAAATATAGTCTAAAAAGGTACAGCTTTTTAGAATCTAGGATACAGCCTTAATTAGAGAGTAAGCATATA +ACACAAACCATAGTTGGCCTAAAAGCAGCCACCAATTAAGAAAGCGTTCAAGCTCAACAATCAAAACATC +TCAATGTCAAAAAACGCAACCAACTCCTAATCTAAAACTGGGCTAATCTATTTAACAATAGAAGCAATAA +TGCTAATATGAGTAACAAGAAATACTTCTCCCGCGCATAAGCTTATATCAGAACGGATAACCACTGATAG +TTAACAACAAGATATATATAACCTAACTACAAGCAAAATATCAGACTAATTGTTAACCCAACACAGGCAT +GCAATTTAGGGAAAGATTAAAAGAAGTAAAAGGAACTCGGCAAACACAAGCCCCGCCTGTTTACCAAAAA +CATCACCTCTAGCATTTCCAGTATTAGAGGCACTGCCTGCCCAGTGACATTAGTTAAACGGCCGCGGTAT +CCTGACCGTGCAAAGGTAGCATAATCATTTGTTCCTTAAATAGGGACTTGTATGAATGGCCACACGAGGG +CTTTACTGTCTCTTACTTCCAATCCGTGAAATTGACCTTCCCGTGAAGAGGCGGGAATACGACAATAAGA +CGAGAAGACCCTGTGGAGCTTTAATTAATCGACCCAAAGAGACCTTAATAACCAACCGACAGGAACAACA +GACCTCTGCCATGGGCCGACAATTTAGGTTGGGGTGACCTCGGAGAATAAAACAACCTCCGAGTGATTTA +AATCTAGACTGACCAGTCGAAAGTATTACATCACTTATTGATCCAAAGCTTGATCAACGGAACAAGTTAC +CCCAGGGATAACAGCGCAATCCTATTTCAGAGTCCATATCGACAATAGGGTTTACGACCTCGATGTTGGA +TCAGGACATCCCGATGGTGCAGCAGCTATCAAAGGTTCGTTTGTTCAACGATTAAAGTCCTACGTGATCT +GAGTTCAGACCGGAGTAATCCAGGTCGGTTTCTATCTATTAAATAATTTCTCCCAGTACGAAAGGACAAG +AGAAATAAGGCCCACTTTACCAAAGCGCCTTTAACCAAATAGATGATATAATCTCAATCTAAACAGTTTA +TCTAAACATATCACCCGTAGAGCTCGGGTTTGTTAGGGTGGCAGAGCCCGGCAATTGCATAAAACTTAAG +CTTTTACTATCAGAGGTTCAACTCCTCTCCCTAACAGCATGTTTATAATCAATATTCTCTCATTAATTAT +CCCTATTCTCTTCGCCGTAGCCTTCCTAACCCTAGTTGAACGTAAAGTACTGGGCTACATACAACTCCGT +AAAGGACCAAACGTCGTAGGACCATACGGCCTACTTCAGCCTATTGCAGACGCCATGAAACTCTTCACTA +AAGAACCCCTCCGACCCCTCACATCCTCCACATTCATATTCATCACAGCACCCATCCTAGCTCTTACACT +AGCCCTAACCATATGAATCCCACTGCCCATACCATACCCACTCATTAACATAAACTTAGGAGTGCTATTT +ATACTAGCTATGTCCAGCCTAGCTGTTTACTCCATTCTATGATCAGGATGGGCTTCAAACTCAAAATATG +CCCTAATCGGAGCCCTACGAGCCGTAGCCCAAACAATCTCATATGAAGTCACATTAGCTATCATTCTCTT +ATCAGTACTACTAATAAATGGATCCTTCACATTAGCTGCACTAATTACCACCCAAGAATACATCTGGCTC +ATCATCCCTGCATGACCCCTAGCCATAATATGATTCATCTCCACACTAGCAGAAACCAACCGAGCTCCAT +TTGATCTAACAGAAGGAGAATCAGAACTCGTTTCCGGATTCAACGTAGAATACGCAGCAGGCCCCTTTGC +CCTATTTTTTCTAGCAGAATACGCTAATATTATCATAATAAACATCCTCACAACAATCTTATTTTTCGGA +GCATTCCATAATCCCTATATACCAGAACTATATACTATCAACTTCACTGTAAAAACCCTAATTCTAACAA +CCACCTTCCTATGGATCCGAGCATCTTATCCACGATTCCGATATGACCAATTAATGCACCTCCTATGAAA +AAACTTCCTACCCCTTACTCTAGCCCTATGCATATGACACGTCTCCCTACCCATCATTACAGCAAGCATT +CCACCCCAAACATAAGAAATATGTCTGACAAAAGAATTACTTTGATAGAGTAAAACATAGAGGTTTAAGC +CCTCTTATTTCTAGAATTATAGGAATCGAACCTAATCCTAAGAATCCAAAAATCTTCGTGCTACCAATAT +TACACCACATTCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTTACAC +CCTTCCCATACTAATCAAACCCCCTATCCTCACCATCATTATACTAACCGTTATCTCAGGAACTATAATC +GTAATAACAACTTCTCACTGACTTATAGTCTGAATTGGCTTCGAAATAAACCTATTAGCTATTATTCCCA +TCCTCATGAAAAAATATAACCCACGAGCCATAGAAGCAGCCACAAAATACTTCCTGACACAAGCAACCGC +TTCAATACTCCTAATAATAGGAATTATCATCAACCTGCTGCACTCAGGACAATGAACCGTATCAAAAGAC +CTCAACCCCATGGCATCCATTATAATAACAACCGCCTTAGCAGTAAAACTAGGACTAGCCCCATTCCACT +TCTGAGTGCCCGAAGTTACACAAGGAATCTCCTTGTCTTCAGGCCTGATCCTACTCACATGACAAAAAAT +CGCACCACTATCAATTCTTTACCAAATTTCACCCACCATTAACCCCAACCTACTCCTAGCAATAGCCATT +ATATCAGTTATAATCGGAGGCTGAGGGGGACTTAACCAAACCCAGCTACGAAAAATCATAGCATACTCCT +CAATCGCCCATATAGGTTGAATAACAGCCATCATAATATATAGCCCCACAATAATAATTTTAAACCTGAC +TATCTATATCATTATAACACTAACCACTTTCATGTTACTCATATACAACTCCACCACAACAACATTATCC +TTATCACAAACATGAAACAAAACGCCCCTGATCACCTCACTTATCCTACTGCTAATAATGTCTCTGGGCG +GCCTCCCCCCACTCTCTGGCTTCATCCCAAAATGAATAATCATTCAAAAACTAACCAAAAATGAAATAAT +CATAATACCCACACTACTAGCCATAACAGCACTACTTAACCTGTACTTCTACATACGACTAACATATACC +ACTGCACTAACTATATTCCCCTCAAACAACTGTATAAAAATAAAATGACGGTTCAAATGCACAAAAAAAA +TAATCTTTTTACCCCCCTTAATCGTAATGTCCACCATGCTACTCCCACTCACACCAATACTATCCGTCCT +AGATTAGAAAGTTTAGGTTAAACTAGACCAAGAGCCTTCAAAGCTCTAAGTAAGCCCTATAGAATTAACT +TCTGCATACCTATTAACTCTAAGGACTGGAAGAATCTATCTTACATCAATTGACTGCAAATCAAACACTT +TAATTAAGCTAAGCCCTTACTAGATTGGTGGGCCCTAACCCCACGAAATTTTAGTTAACAGCTAAATACC +CTAATCAACTGGCTTCAATCTACTTCTCCCGCCGCCTGGAAAAAAAAGGCGGGAGAAGCCCCGGCAGCGT +CAAGCTGCTTCTTTGAATTTGCAATTCAATATGACATTCACTACAGGACTTGGTAAAAAGAGGGTTAGAA +CCTCCTGTCTTTAGATTTACAGTCTAATGCTTACTCAGCCATTTTACCTATGTTCATAAACCGCTGACTA +TTTTCAACCAATCACAAGGATATTGGAACTCTTTACCTTTTATTTGGCGCCTGGGCTGGTATAGTGGGGA +CTGCCCTCAGTCTCCTAATTCGAGCCGAACTGGGTCAACCTGGCACACTACTAGGAGATGACCAAATTTA +TAATGTAGTAGTTACTGCCCATGCCTTTGTGATAATCTTTTTTATAGTAATGCCTATTATAATTGGAGGA +TTCGGAAACTGGCTAGTTCCGTTAATAATCGGAGCCCCCGATATGGCATTCCCTCGAATGAATAACATAA +GCTTCTGACTCCTTCCCCCATCCTTCCTACTTCTGCTCGCATCGTCTATGGTAGAAGCTGGGGCAGGAAC +TGGGTGGACAGTATACCCACCCCTAGCTGGCAACCTAGCCCATGCAGGAGCATCCGTGGATCTAACTATT +TTTTCACTACACCTAGCAGGCGTCTCCTCAATCTTAGGTGCTATTAATTTTATTACTACTATTATTAATA +TAAAACCGCCCGCTATGTCCCAATACCAAACACCCCTGTTTGTTTGATCGGTTCTAATTACTGCTGTGTT +GCTACTTCTATCACTGCCAGTTTTAGCAGCAGGCATCACCATGCTACTGACAGATCGAAATCTAAATACC +ACATTTTTTGATCCTGCCGGGGGAGGAGACCCCATCTTATATCAACACCTATTCTGATTCTTCGGTCACC +CAGAAGTCTATATCTTAATCCTGCCCGGGTTTGGAATAATTTCACATATTGTCACCTACTACTCAGGCAA +AAAAGAACCTTTTGGCTACATGGGGATAGTCTGAGCCATAATGTCAATTGGCTTTCTGGGCTTTATCGTA +TGGGCCCATCACATGTTTACTGTAGGGATAGATGTGGATACACGAGCATACTTTACGTCAGCTACTATAA +TTATCGCTATTCCTACTGGGGTAAAAGTATTTAGCTGATTGGCCACTCTTCACGGGGGTAATATTAAATG +GTCTCCCGCTATACTATGGGCTTTGGGATTCATTTTCCTATTCACCGTAGGGGGCTTAACAGGAATTGTA +CTAGCAAACTCCTCATTGGATATTGTCCTTCACGACACATACTACGTAGTAGCCCACTTCCACTACGTCT +TGTCAATAGGAGCAGTATTTGCTATTATAGGGGGCTTCGTTCACTGATTCCCCTTATTCTCAGGGTATAC +TCTTGATAATACTTGGGCAAAAGTTCATTTTACGATCATGTTCGTAGGTGTCAATATAACGTTTTTCCCT +CAGCATTTCCTAGGCCTGTCTGGGATGCCTCGACGTTATTCTGACTATCCAGACGCGTATACAACTTGAA +ACACAATCTCCTCAATAGGCTCTTTTATTTCACTAACAGCAGTAATATTAATAGTCTTTATAATGTGAGA +AGCTTTCGCATCAAAGCGAGAAGTAGCCACAGTGGAACTAACCACAACTAATCTCGAATGACTTCACGGA +TGTCCTCCTCCGTATCACACATTTGAAGAGCCAGCCTACGTGCTGTTAAAATAAGAAAGGAAGGAATCGA +ACCTCCTTAGACTGGTTTCAAGCCAATACCATAACCACTATGTCTTTCTCAATTAAGAAGTATTAGTAAA +ATAATTACATAACTTTGTCAAAGTTAAATTATAGGTTTAAGCCCTATGTGCTTCCATGGCATACCCCTTC +CAACTAGGTTTTCAAGATGCTACATCCCCCATTATAGAAGAGCTTTTACACTTCCATGATCATACATTAA +TAATTGTATTCCTAATTAGCTCCCTAGTCCTCTACATTATCTCATTAATACTGACAACTAAACTTACGCA +TACAAGCACAATAGATGCCCAAGAAGTAGAAACTATCTGAACCATTTTACCAGCCATCATCTTAATTCTC +ATTGCCCTGCCTTCCTTACGAATTCTCTATATAATAGATGAGATTAATAATCCCTCCCTCACTGTAAAGA +CTATAGGACATCAGTGATACTGAAGTTATGAGTACACCGACTATGAGGACCTAAGCTTCGACTCCTACAT +AATCCCCACTCAAGAGTTAAAGCCCGGAGAGCTCCGACTACTAGAAGTTGATAACCGAGTAGTGTTGCCA +ATAGAAGTGACTATTCGCATGTTAGTCTCATCAGAGGACGTACTGCACTCGTGAGCCATCCCATCCCTGG +GCCTAAAAACTGACGCTATCCCAGGCCGACTAAACCAAACAACCCTAATAGGCACACGGCCTGGGCTATA +TTATGGTCAGTGCTCAGAAATCTGCGGCTCAAATCACAGTTTTATGCCCATTGTCCTTGAACTAGTCCCG +CTGTCATATTTCGAAAAATGATCTGCATCTATGCTGTAATTTCACTAAGAAGCTAAATTAGCGTTAACCT +TTTAAGTTAAAAACTGGGAGTTCAAACCTCCCCTTAGTGACATGCCACAGTTAGACACATCAACCTGATT +TATTACTATTATTTCAATAATCATGACACTGTTCGTTATATTTCAACTAAAAATCTCAAAACATCTGTAC +CCATCAAGCCCAGAACCCAAATCTACAGCTGCATTAAAACAGCCGAGTCCCTGAGAAAAAAAATGAACGA +AAATCTATTCACCTCTTTTACTACCCCAACAATAATAGGACTGCCTGTTGTTGTGTTAATCGTTATGTTC +CCCAGCATTCTATTTCCCTCGCCTAACCGACTAATTAATAACCGCCTAGTCTCACTCCAACAATGATTAG +TACAACTTACATTAAAGCAAATACTGATTACCCACAATTACAAAGGACAAACCTGGGCCCTAATACTTAT +GTCTCTCATTTTATTTATTGGGTCAACAAATCTGCTAGGTCTACTACCTCACTCATTTACTCCAACTACC +CAATTATCAATAAACCTAGGCATAGCCATCCCCTTGTGAGCCGGCACCGTAATCACTGGATTCCGTCACA +AAACTAAAGCATCCTTGGCCCACTTTCTACCACAAGGAACACCAGTCCCCTTAATCCCTATGCTCGTAAT +TATCGAAACTATCAGCCTTTTTATCCAGCCCGTAGCCCTAGCCGTACGACTCACAGCTAATATTACTGCA +GGCCATTTATTAATACACCTAATCGGAGGAGCTGCTTTAGCCCTAACAAATATTAGTGCCCCTACTGCTT +TAATTACCTTTATCATCCTCATCCTACTGACAATTCTTGAATTCGCTGTAGCTCTAATCCAAGCCTATGT +TTTTACCCTACTTGTGAGCCTGTATTTACATGATAATACTTAATGACCCACCAAACCCACGCATATCACA +TGGTTAATCCCAGCCCATGGCCACTTACAGGGGCCCTTTCGGCCCTACTAATAACCTCAGGCCTGGCTAT +ATGATTTCACTATAACTCAATACTACTATTAACTCTAGGAATAACCACTAACCTATTGACTATATACCAA +TGGTGACGAGACATCATTCGGGAGAGCACATTCCAAGGCCACCACACACCCATTGTTCAAAAAGGCCTCC +GATACGGAATAATCCTTTTCATCATCTCAGAAGTATTCTTCTTCGCAGGTTTTTTCTGGGCCTTCTATCA +CTCAAGCCTGGCCCCGACCCCCGAATTGGGAGGATGCTGGCCACCAACAGGTATTATTCCCCTAAACCCC +CTAGAAGTCCCACTACTCAATACTTCTGTGCTCTTAGCTTCCGGAGTGTCAATCACCTGAGCCCATCATA +GCCTAATAGAAGGAAATCGAAAACACATGCTCCAAGCACTATTTATTACAATCTCCCTAGGAGTCTATTT +TACCCTCCTCCAAGCCTCTGAGTACTATGAAACATCATTTACAATCTCGGACGGAGTTTATGGGTCCACC +TTTTTCATAGCCACAGGGTTCCACGGACTACACGTAATTATTGGCTCTACCTTCCTAATCGTATGTTTCT +TGCGCCAACTAAAATACCACTTCACATCGAGCCACCATTTTGGATTCGAAGCCGCTGCTTGATATTGACA +TTTCGTAGACGTGGTTTGACTGTTCTTATACGTTTCCATTTATTGATGAGGATCCTATTCCCTTAGTATC +AACAAGTACAGTTGACTTCCAATCAACCAGTTTCGGTATAATCCGAAAGGGAATAATAAACATAATACTC +GCTCTACTCACCAACACACTTCTATCCACACTACTTGTACTCATCGCGTTCTGACTACCCCAACTAAACA +CCTATGCAGAAAAAGCAAGTCCTTATGAATGTGGATTTGACCCCATAGGATCCGCTCGCCTGCCCTTCTC +CATAAAATTCTTCCTAGTAGCTATCACATTCTTGCTATTCGACCTAGAAATTGCACTACTGCTCCCTCTT +CCCTGAGCCTCACAAACAAACAAACTGTCAACCATGCTTATCACAGCCCTTCTACTAATCTCCCTATTAG +CCGCAAGCCTAGCCTACGAGTGAACCCAAAAAGGATTAGAATGAACTGAATATGATAATTAGTTTAAACT +AAAACAAATGATTTCGACTCATTAGATTGTAGCTTACCCTATAATTATCAAATGTCCATAGTCTATGTTA +ACATCTTCCTGGCTTTCATCGTATCACTCATAGGACTATTAATGTACCGATCCCACTTAATATCCTCCCT +TCTATGCCTAGAAGGCATAATACTATCCCTATTTATTATGATAACCATGGCAGTTCTAAACAATCACTTT +ACACTAGCTAGCATGACCCCCATTATCCTGCTAGTATTTGCAGCCTGCGAGGCAGCACTGGGCTTGTCCC +TACTAGTAATGGTATCAAATACATATGGTACCGACTATGTACAAAACCTAAACCTCTTGCAATGCTAAAA +ATTATTATCCCCACTGCCATACTCATACCAATAACATGATTATCAAAACCCAGCATAATCTGAATTAACT +CAACCACCTATAGTTTTCTGATCAGCCTTGTTAGCCTGTCCTACTTAAATCAACTAGGCGACAACAGCCT +AAATCTCTCATTACTATTTTTCTCAGACTCACTCTCTGCACCCCTACTAGTATTAACAACATGACTCTTA +CCACTAATGCTCATGGCTAGTCAATCACACCTGTCAAAAGAGACCCTAGCCCGAAAAAAACTATACATTA +CAATACTTATTATCCTACAACTCCTCTTAATTATAACATTCACCGCTACAGAACTGATTATATTCTACAT +TCTATTCGAAGCTACATTAATCCCTACTCTTATTATTATCACTCGATGAGGCAATCAAACAGAGCGACTA +AACGCTGGTCTGTACTTTCTATTCTACACCCTGGTAGGCTCACTACCCCTCCTAGTCGCACTACTATACA +TCCAAAACACAACAGGAACTCTGAACTTCCTAATTATTCAATACTGAGCCAAACCAATTTCAGCCACCTG +ATCTAATATCTTTCTCTGACTAGCATGCATAATAGCATTCATAGTAAAAATACCTCTATATGGGCTCCAC +CTGTGACTACCAAAAGCACATGTCGAAGCTCCCATTGCCGGCTCAATAGTCCTTGCTGCTGTACTGTTGA +AGCTAGGAGGATATGGAATGATACGCATTACAATCCTACTCAACCCCACAACAAACCAAATGGCATACCC +CTTCATAATGCTATCCCTATGGGGAATAATTATAACAAGCTCTATTTGTCTACGCCAGACAGACCTAAAA +TCCCTAATCGCATATTCATCCGTAAGCCATATGGCCCTAGTAATCGTGGCCGTACTAATTCAAACACCTT +GGAGTTACATAGGAGCCACAGCTCTTATAATCGCCCACGGACTAACTTCCTCAGTGCTATTTTGCCTTGC +AAACTCAAACTACGAACGAATCCATAGCCGAACAATAATTCTCGCACGAGGCCTACAAACCATCCTCCCC +CTAATAGCTGCTTGATGACTACTGGCCAGCCTCGCAAACCTGGCCCTACCTCCTACTATTAACCTAATTG +CAGAGCTATTTGTAGTAGTGGCCTCCTTTTCATGATCTAACATAACCATTACTCTCATGGGCACAAATAT +CATCATCACAGCCCTATATACCCTCTACATACTCATTACAACCCAACGAGGCAAATATACACACCACATT +AAAAACATCAATCCATCATTCACACGAGAAAATGCCCTAATAACACTTCATCTGCTCCCACTTTTTCTCT +TATCTCTCAACCCCAAAATCGTACTAGGTCCTATTTACTGTAAATATAGTTTAATAAAAACATTAGATTG +TGAATCTAATAATAGAAGTGCAAATCTTCCTATTTAAACGAAAAAGTATGCAAGAGCTGCTAACTCATGC +CCCCACGTATAAAAACGTGGCTTTTTCAACTTTTATAGGATAGAAGTAATCCATTGGTCTTAGGAGCCAA +AAAATTGGTGCAACTCCAAATAAAAGTAATAAACCTACTTACCTCCTCTATACTCACTGCGATATTTATC +CTACTCCTACCTATCATTACATCCAACACTCAATTATATAAAAGTAACCTATACCCTCACTATGTAAAAA +CCACAATCTCTTACGCCTTTACCATTAGTATAATCCCAGCCATAATATTCATTTCCTCCGGACAAGAGAT +AACCATCTCAAACTGATGTTGACTATCAATTCAAACCCTTAAATTATCACTAAGCTTCAAACTAGATTAT +TTCTCGATCATCTTCATCCCAGTAGCACTTTTCGTTACATGGTCGATCATAGAATTCTCAATGTGATACA +TACACACAGATCCCTATATTAACCAGTTCTTTAAGTACCTCCTTATATTCCTAATCACTATAATGATCTT +AGTGACCGCCAATAATCTATTTCAGCTGTTTATTGGATGGGAGGGAGTAGGAATTATATCTTTCCTACTT +ATCGGATGATGATATGGTCGAGCAGACGCAAACACTGCCGCCCTGCAAGCAATTCTCTACAACCGTATTG +GTGATGTAGGATTTATCATGGCCATAGCATGATTCCTTACCAACCTAAATGCATGAAACCTCCAACAAAT +CTTTATCACTCAACATGAAAGCCTGAATATGCCATTACTAGGACTCCTCCTAGCCGCCACAGGCAAGTCC +GCCCAATTTGGCCTACACCCATGATTGCCATCAGCCATAGAAGGTCCAACTCCCGTCTCCGCCCTACTCC +ACTCAAGCACAATAGTTGTAGCCGGAGTCTTCTTATTAATCCGCTTCCACCCACTCATAGAACAAAATAA +AGCCATACAAACCCTCACTCTATGCCTGGGGGCCATCACAACCCTATTCACAGCCATCTGTGCCCTCACA +CAAAATGATATTAAAAAAATTGTTGCTTTCTCAACTTCAAGCCAATTAGGCCTGATAATCGTTACTATCG +GAATTAACCAACCCTACCTTGCATTCCTGCATATCTGCACACACGCATTTTTTAAAGCCATATTATTCAT +GTGCTCCGGATCAATTATCCACAGTCTAAACGACGAGCAAGATATTCGAAAAATAGGCGGACTATATAAA +CCAATACCCTTTACTACCACCTCCCTTATTATCGGAAGCCTCGCATTAACAGGCATGCCATTCCTAACAG +GCTTTTACTCCAAAGACCTAATCATCGAGACAGCCAATACGTCGTATACCAACGCCTGAGCCCTATTGGT +CACTCTCATTGCTACATCCCTCACAGCCGCCTATAGTACTCGAATCATATTCTTTGCACTCCTGGGGCAA +CCCCGATTCAACTCCCTAAGCCCAATCAATGAAAACAACCCCCACCTCATCAACTCCATTAAACGTCTCT +TAATTGGAAGCATTTTTGCAGGATACTTGATCTCCCATAACATCCCCCCAACGACCATCCCACAAATGAC +CATACCCTGCCACCTAAAACTAACTGCTCTCGCCATGACCATCATAGGCTTTATCCTGGCATTAGAGCTT +AACCTCGTGGCTAAAAACTTAAAATTTAAATACCCCTCAAATCTTTTTAAGTTTTCTAACCTCCTCGGGT +ACTTTCCAATCGTAATTCACCGCCTCCCATCGATAATAAGCCTAACCATAAGCCAAAAATCCGCATCGAT +ACTATTAGATATAATCTGGCTAGAAAATGTAATACCAAAATCCATCTCCCACTTCCAAATAAAAATATCA +ACCGCCGTATCTAATCAGAAGGGACTAGTTAAGCTCTACTTCCTATCCTTCATAATCACCCTGACCCTTA +GCCTACTCTTACTTAGTTTCCACGAGTAACCTCTATAATCACCAATACACCAATAAGCAAAGACCAACCA +GTGACAACCACTAGCCAGGTTCCATAACTATACAGTGCTGCAATTCCTATGGCCTCCTCACTAAAAAACC +CCGAGTCACCCGTATCATAGATCACTCAATCACCCGCACCATTAAACTTAAACACAACCTCAACCTCATC +TTCCTTTAAAATATAGCAAGCAGTCAACAACTCCGCTAATACCCCCGTAATAAACGCACCTAATACGGCT +TTATTAGATGTCCACGCCTCGGGGTAGGGCTCAGTAGCCATAGCTGTAGTGTACCCAAACACCACAAGCA +TGCCCCCCAAATAAATTAAAAAAACTATTAAACCTAAAAATGACCCCCCAAAATTCAATACAATACCGCA +ACCAACACCACCAGCCACAATCAATCCAAGCCCACCATAAATAGGAGAAGGCTTTGAAGAAAAACTCACA +AAGCTCACCACGAAAATTGTACTTAAAATAAATACAATGTATGTTATCATAATTCTCACATGGATTCTAA +CCACGACCAATGATATGAAAAACCATCGTTGTATTTCAACTATAAGAACTTAATGACCAACATTCGAAAA +TCACACCCCCTTATCAAAATTATTAATCACTCATTTATTGACCTACCCGCCCCATCCAATATTTCAGCAT +GATGAAACTTTGGCTCCTTACTAGGGGTGTGCTTAATCTTACAAATCCTCACTGGCCTCTTTCTAGCCAT +ACACTACACATCAGACACAATAACCGCTTTCTCATCAGTTACCCACATTTGCCGCGACGTAAACTACGGC +TGGATTATCCGATATCTACATGCCAACGGAGCCTCCATATTCTTTATCTGTCTATACATGCACGTAGGAC +GAGGAATATACTACGGCTCCTACACCTTCTCAAAAACATGAAATATCGGGATTGTGCTATTGTTTACGGT +CATGGCTACAGCCTTCATAGGATATGTCTTACCATGAGGACAAATATCATTCTGAGGGGCAACCGTAATC +ACCAACCTCCTGTCAGCAATCCCATATATTGGGACCGACCTAGTAGAGTGAATCTGAGGGGGTTTCTCAG +TAGACAAAGCTACCCTGACACGATTCTTTGCCTTCCACTTCATCCTTCCGTTTATCGTCTCAGCCCTAGC +AGCAGTCCACCTCCTATTCCTTCACGAAACAGGATCCAATAACCCCTCAGGAATGGTGTCCGACTCAGAC +AAAATCCCATTCCACCCATACTACACAATTAAAGATATCTTAGGCCTCTTAGTACTAATCCTAACCCTCA +CACTACTCGTCCTATTCTCACCAGACCTATTAGGAGACCCTGATAACTACATCCCCGCCAACCCCCTAAA +TACCCCTCCCCATATTAAGCCCGAATGGTATTTCCTATTCGCATACGCAATCCTCCGATCTATTCCCAAT +AAACTAGGAGGAGTTCTAGCCCTAGTCTTATCCATCTTAATCTTAGCCACTATCCCTGCCCTCCACACAT +CCAAACAACGAGGAATAATGTTTCGACCGCTAAGCCAATGCTTATTCTGACTCTTAGTGGCAGACCTTCT +AACCCTAACATGAATTGGTGGCCAACCTGTAGAACACCCCTTTATTGCCATCGGCCAACTAGCCTCTATC +CTATACTTCTTCATCCTCCTAGTCTTAATCCCCATCTCAGGCATTATTGAAAACCGCCTCCTTAAATGAA +GAGTCTTCGTAGTATATAAATTACTTTGGTCTTGTAAACCAAAAAAGGAGAATATGTACTCTCCCTAAGA +CTTCAAGGAAGAAGCAATAGCCCCACCATCAGCACCCAAAGCTGAAATTCTTTCTTAAACTATTCCTTGC +CAATACCAAAAAACAACCCCATGACTTTCATAATTCATATATTGCATATACCCGTACTGTGCTTGCCCAG +TATGTCCTCATCCCCACAAAAAATAAGTGAAAAAATCCTCAATCCCCGTTAATACAGAACACACAACACG +AAATAACCTGTTAACTACCGGACCCCCCCCCTCCCCCCGTTAACACATTACGTAGGGCATACTATGTATA +TCGGGCATTAATCGCCTGTCCCCATGAATATTAAGCATGTACAGTAGTTTATATATTTTACATAAGGCAT +ACTATGTATATCGTGCATTAATCCCTTGTCCCCATGAATATTAAGCATGTACAGTAGTTCATATATATTA +CATAAAACATAATAGTGCTTAATCGTGCATATTCATGATTTAAAACAGTTCTTTCATGGATCTCAACTAT +CCGAAAAAGCTTAATCACCTGGCCTCGAAAAACCAACAACCCTTGCTCGAGCGTGTACCTCTTCTCGCTC +CGGGCCCATTTCAACGTGGGGGTGTCTATAGTGAAACTATACCTGGCATCTGGTTCTTACTTCAGGGTCA +TGACATTCTTAAATCCAATCCTTCAACTTTCTCAAATAGGACATCTCGAT +
--- a/tools/clc_assembly_cell/README.rst Fri Nov 15 11:44:54 2013 -0500 +++ b/tools/clc_assembly_cell/README.rst Fri Nov 21 06:40:45 2014 -0500 @@ -47,22 +47,23 @@ First install the CLC Assembly Cell sortware as described above. To install the wrapper copy or move the following files under the Galaxy tools -folder, e.g. in a tools/clcbio folder: +folder, e.g. in a ``tools/clcbio/`` folder: * clc_assembler.xml (Galaxy tool definition) * clc_mapper.xml (Galaxy tool definition) * README.rst (this file) -You will also need to modify the tools_conf.xml file to tell Galaxy to offer the -tools. Just all these line, for example next to other assembly tools:: +You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer +the tools. Just all these line, for example next to other assembly tools:: <tool file="clc_assembly_cell/clc_assembler.xml" /> <tool file="clc_assembly_cell/clc_mapper.xml" /> -If you wish to run the unit tests, also add this to tools_conf.xml.sample -and move/copy the test-data files under Galaxy's test-data folder. Then:: +If you wish to run the unit tests, also move/copy the ``test-data/`` files +under Galaxy's ``test-data/`` folder. Then run:: - $ ./run_functional_tests.sh -id clc_assembler + $ ./run_tests.sh -id clc_assembler + $ ./run_tests.sh -id clc_mapper That's it. @@ -73,7 +74,9 @@ ======= ====================================================================== Version Changes ------- ---------------------------------------------------------------------- -v0.0.1 - Initial public release +v0.0.1 - Initial public release. +v0.0.2 - Actually use the ``$CLC_ASSEMBLY_CELL`` environment variable. + - Enable and fixed the tests. ======= ====================================================================== @@ -86,7 +89,7 @@ For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use the following command from the Galaxy root folder:: - $ tar -czf clcbio.tar.gz tools/clc_assembly_cell/README.rst tools/clc_assembly_cell/clc_assembler.xml tools/clc_assembly_cell/clc_mapper.xml tools/clc_assembly_cell/repository_dependencies.xml + $ tar -czf clcbio.tar.gz tools/clc_assembly_cell/README.rst tools/clc_assembly_cell/clc_assembler.xml tools/clc_assembly_cell/clc_mapper.xml tools/clc_assembly_cell/tool_dependencies.xml test-data/NC_010642.fna Check this worked:: @@ -94,7 +97,8 @@ tools/clc_assembly_cell/README.rst tools/clc_assembly_cell/clc_assembler.xml tools/clc_assembly_cell/clc_mapper.xml - tools/clc_assembly_cell/repository_dependencies.xml + tools/clc_assembly_cell/tool_dependencies.xml + test-data/NC_010642.fna Licence (MIT)
--- a/tools/clc_assembly_cell/clc_assembler.xml Fri Nov 15 11:44:54 2013 -0500 +++ b/tools/clc_assembly_cell/clc_assembler.xml Fri Nov 21 06:40:45 2014 -0500 @@ -1,10 +1,10 @@ -<tool id="clc_assembler" name="CLC assembler" version="0.0.1"> +<tool id="clc_assembler" name="CLC assembler" version="0.0.2"> <description>Assembles reads giving a FASTA file</description> <requirements> <requirement type="binary">clc_assembler</requirement> </requirements> - <version_command>/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/clc_assembler | grep -i version</version_command> - <command>/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/clc_assembler + <version_command>\${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_assembler | grep -i version</version_command> + <command>\${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_assembler #for $rg in $read_group ##-------------------------------------- #if str($rg.segments.type) == "paired" @@ -25,7 +25,7 @@ #end for -m $min_contig_len -o "$out_fasta" ---cpus \$GALAXY_SLOTS +--cpus \${GALAXY_SLOTS:-4} -v | grep -v "^Progress: "</command> <stdio> <!-- Assume anything other than zero is an error --> @@ -37,7 +37,7 @@ <conditional name="segments"> <param name="type" type="select" label="Are these paired reads?"> <option value="paired">Paired reads (as two files)</option> - <option value="interleaved">Paired reads (as one interleaved file)</option> + <option value="interleaved">Paired reads (as one interleaved file)</option> <option value="none">Unpaired reads (single or orphan reads)</option> </param> <when value="paired"> @@ -47,7 +47,7 @@ <option value="ff">---> ---></option> <option value="bb"><--- <---</option> </param> - <param name="dist_mode" type="select" label="How is the fragment distance measured?"> + <param name="dist_mode" type="select" label="How is the fragment distance measured?"> <option value="ss">Start to start (e.g. Sanger capillary or Solexa/Illumina libraries)</option> <option value="se">Start to end</option> <option value="es">End to start</option> @@ -58,7 +58,7 @@ label="Minimum size of 'good' DNA templates in the library preparation" /> <param name="max_size" type="integer" optional="false" min="0" value="" label="Maximum size of 'good' DNA templates in the library preparation" /> - <param name="filename1" type="data" format="fastq,fasta" required="true" label="Read file one"/> + <param name="filename1" type="data" format="fastq,fasta" required="true" label="Read file one"/> <param name="filename2" type="data" format="fastq,fasta" required="true" label="Read file two"/> </when> <when value="interleaved"> @@ -84,13 +84,13 @@ <when value="none"> <param name="filenames" type="data" format="fastq,fasta" multiple="true" required="true" label="Read file(s)" help="Multiple files allowed, for example several files of orphan reads." /> - </when> + </when> </conditional> </repeat> - <param name="min_contig_len" type="integer" optional="false" min="1" value="200" label="Minimum contig length"/> - <!-- Word size? --> - <!-- Bubble size? --> - <!-- Scaffolding options? --> + <param name="min_contig_len" type="integer" optional="false" min="1" value="200" label="Minimum contig length"/> + <!-- Word size? --> + <!-- Bubble size? --> + <!-- Scaffolding options? --> <!-- AGP / GFF output? --> </inputs> <!-- min/max validation? <code file="clc_validator.py" /> --> @@ -98,19 +98,17 @@ <data name="out_fasta" format="fasta" label="CLCbio assember contigs (FASTA)" /> </outputs> <tests> - <!-- Review this test once Galaxy handles repeat groups better <test> - <param name="type" value="interleaved" /> - <param name="placement" value="fb" /> - <param name="dist_mode" value="ss" /> - <param name="min_size" value="1" /> - <param name="max_size" value="1000" /> - <param name="dist_mode" value="ss" /> - <param name="filename" value="SRR639755_mito_pairs.fastq.gz" ftype="fastqsanger" /> + <param name="read_group_0|segments|type" value="interleaved" /> + <param name="read_group_0|segments|placement" value="fb" /> + <param name="read_group_0|segments|dist_mode" value="ss" /> + <param name="read_group_0|segments|min_size" value="1" /> + <param name="read_group_0|segments|max_size" value="1000" /> + <param name="read_group_0|segments|dist_mode" value="ss" /> + <param name="read_group_0|segments|filename" value="SRR639755_mito_pairs.fastq.gz" ftype="fastqsanger" /> <param name="min_contig_len" value="200" /> <output name="out_fasta" file="SRR639755_mito_pairs.clc4_de_novo.fasta" ftype="fasta" /> </test> - --> </tests> <help>
--- a/tools/clc_assembly_cell/clc_mapper.xml Fri Nov 15 11:44:54 2013 -0500 +++ b/tools/clc_assembly_cell/clc_mapper.xml Fri Nov 21 06:40:45 2014 -0500 @@ -1,4 +1,4 @@ -<tool id="clc_mapper" name="CLC Mapper" version="0.0.1"> +<tool id="clc_mapper" name="CLC Mapper" version="0.0.2"> <description>Maps reads giving a SAM/BAM file</description> <requirements> <requirement type="binary">clc_mapper</requirement> @@ -6,9 +6,9 @@ <requirement type="binary">samtools</requirement> <requirement type="package" version="0.1.19">samtools</requirement> </requirements> - <version_command>/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/clc_mapper | grep -i version</version_command> + <version_command>\${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_mapper | grep -i version</version_command> <command>echo Mapping reads with clc_mapper... -&& /mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/clc_mapper +&& \${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_mapper #for $ref in $references #if str($ref.ref_type)=="circular" -d -z "$ref.ref_file" @@ -35,7 +35,7 @@ ##-------------------------------------- #end for -o "temp_job.cas" ---cpus \$GALAXY_SLOTS +--cpus \${GALAXY_SLOTS:-4} ## TODO - filtering out the progress lines seems to mess up the multiple commands ## | grep -v "^Progress: " ##=========================================== @@ -59,7 +59,7 @@ <!-- Job splitting with merge via clc_join_mappings? --> <inputs> <!-- Support linear and circular references (-z) --> - <repeat name="references" title="Reference Sequence" min="1"> + <repeat name="references" title="Reference Sequence" min="1"> <param name="ref_file" type="data" format="fasta" required="true" label="Reference sequence(s) (FASTA)" /> <param name="ref_type" type="select" label="Reference type"> <option value="linear">Linear (e.g. most chromosomes)</option> @@ -131,27 +131,26 @@ <data name="out_bam" format="bam" label="CLCbio mapping (BAM)" /> </outputs> <tests> - <!-- TODO, actually test this... tricky due to single machine licence + <!-- CLC's SAM header @PG and @RG lines include filenames so will change --> <test> <param name="ref_file" value="NC_010642.fna" ftype="fasta" /> <param name="ref_type" value="circular" /> - <param name="type" value="interleaved" /> - <param name="placement" value="fb" /> - <param name="dist_mode" value="ss" /> - <param name="min_size" value="1" /> - <param name="max_size" value="1000" /> - <param name="dist_mode" value="ss" /> - <param name="filename" value="SRR639755_mito_pairs.fastq.gz" ftype="fastqsanger" /> - <output name="out_fasta" file="SRR639755_mito_pairs_vs_NC_010642_clc.bam" ftype="bam" /> + <param name="read_group_0|segments|type" value="interleaved" /> + <param name="read_group_0|segments|placement" value="fb" /> + <param name="read_group_0|segments|dist_mode" value="ss" /> + <param name="read_group_0|segments|min_size" value="1" /> + <param name="read_group_0|segments|max_size" value="1000" /> + <param name="read_group_0|segments|dist_mode" value="ss" /> + <param name="read_group_0|segments|filename" value="SRR639755_mito_pairs.fastq.gz" ftype="fastqsanger" /> + <output name="out_fasta" file="SRR639755_mito_pairs_vs_NC_010642_clc.bam" ftype="bam" lines_diff="4"/> </test> - --> </tests> <help> **What it does** Runs the CLCbio tool ``clc_mapper`` which produces a proprietary binary -CAS format file, which is immediately processed using ``cls_cas_to_sam`` +CAS format file, which is immediately processed using ``clc_cas_to_sam`` to generate a self-contained standard BAM file, which is then sorted and indexed using ``samtools``.
--- a/tools/clc_assembly_cell/repository_dependencies.xml Fri Nov 15 11:44:54 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -<?xml version="1.0"?> -<repositories description="This requires samtools (to generate a BAM file)"> - <repository changeset_revision="54195f1d4b0f" name="package_samtools_0_1_19" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> -</repositories>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/clc_assembly_cell/tool_dependencies.xml Fri Nov 21 06:40:45 2014 -0500 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="samtools" version="0.1.19"> + <repository changeset_revision="632f1a03db92" name="package_samtools_0_1_19" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>