# HG changeset patch
# User peterjc
# Date 1416570045 18000
# Node ID 93ef6468b2887d3132e19a9cdef36372b797acb6
# Parent  6e145e4715a7e9ed2afc2a15e8af834b824b936d
Uploaded v0.0.2 which uses the described environment variable to find the binaries

diff -r 6e145e4715a7 -r 93ef6468b288 test-data/NC_010642.fna
--- /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
+
diff -r 6e145e4715a7 -r 93ef6468b288 tools/clc_assembly_cell/README.rst
--- 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)
diff -r 6e145e4715a7 -r 93ef6468b288 tools/clc_assembly_cell/clc_assembler.xml
--- 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">---&gt; ---&gt;</option>
                         <option value="bb">&lt;--- &lt;---</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>
 
diff -r 6e145e4715a7 -r 93ef6468b288 tools/clc_assembly_cell/clc_mapper.xml
--- 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...
-&amp;&amp; /mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/clc_mapper
+&amp;&amp; \${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``.
 
diff -r 6e145e4715a7 -r 93ef6468b288 tools/clc_assembly_cell/repository_dependencies.xml
--- 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>
diff -r 6e145e4715a7 -r 93ef6468b288 tools/clc_assembly_cell/tool_dependencies.xml
--- /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>