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blast.jdl

JobType = "Parametric";

Executable = "blast.sh";

Arguments = "bosTau7_chr1_44272457_44273235_+.fa _PARAM_";

Parameters = 28;

ParameterStart = 0;

ParameterStep = 1;

StdOutput = "std.out";

StdError = "std.err";

InputSandbox = {"blast.sh","bosTau7_chr1_44272457_44273235_+.fa"};

OutputSandbox = {"std.out","std.err","result.xml"};

Requirements   = Member("VO-academicgrid-BLAST_PLUS", other.GlueHostApplicationSoftwareRunTimeEnvironment);

 

 

blast.sh
#!/bin/bash

FRAG_NUMBER=$(printf %02d $2)
$VO_ACADEMICGRID_SW_DIR/blast+/bin/blastn -query $1 -db nt.$FRAG_NUMBER -outfmt 7 -out result.xml

bosTau7_chr1_44272457_44273235_+.fa

>bosTau7_chr1_44272457_44273235_+

CCAGGAGGAAATTCTGTGTATGGACGAAAGGACTGCAACATGTCCTAAGAATTGAAAACTGGCAACTATGATGTAACAACTGCAG

AAGATTCAGGCTTGTTTTCCATGTTTTTAACTCTCCAAAAGGGATAATACATTAAGGGGATAATACAGCCAAAGAAGGGATGATATA

AAAAATCACAGGAAATTAAATGAGTACAAAAACAGTACAAAGATCACGAGAACTTGAGAAGGTATGAAAAACCAAGCAGCGACAAG

GCAGCTCCCTGGAGTTGCACCAGGCCTGACTGTTCCCTGTCCTACACGAAACTGGTGGACTCTTCATCTGGGCATTTCAGTCT

GAGAAATCAGCCAGATTCATGATTTTTAAACAAAGGTTTACTTAGATACAACTTAGGGAGAGAAAGCTAAACATTCGGAAAGTATTA

ACTCCTTGAGAAATCAAAATTGTGCAGCCAAATGAAAGCAAAGTATAAAATCTGGATAAAAATGTTTCTCTAAAGGTAAAATTCAGC

TTCCTGAGAGATTTCAAATCAAACACATAGTAAGAGAGTGGTTTTCAAAGTGGGTTTCAGGCCCATCCTCTCTTCAAACTTTTCT

TATACCCAAACACTTCTAATTCTGTTTTTATCTTCTGTGGTTTCAGCAAACATCTCCTTTTTTAAAAAAAAAAGGAAATCTGATGCC

ACCTCCATCCCTTTGCTATTGTTTGTTCTTTTAAATTTAAAAATCACTGCTATGAGAAAAATGAGATCTATGACATACTTTGTCAGT

ATTAC

 



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