| Previous changeset 7:04e3bba317f4 (2014-06-05) Next changeset 9:3b27cae9b359 (2014-07-14) |
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Commit message:
Corrected macro.xml handling of GALAXY_URL |
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modified:
VCF_to_VariantDB.pl VCF_to_VariantDB.xml VCF_to_VariantDB_macros.xml |
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| diff -r 04e3bba317f4 -r db44ff975de8 VCF_to_VariantDB.pl --- a/VCF_to_VariantDB.pl Thu Jun 05 04:02:28 2014 -0400 +++ b/VCF_to_VariantDB.pl Tue Jun 10 06:01:18 2014 -0400 |
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| @@ -111,10 +111,13 @@ ## link files $vcfurl = "$dd/data.vcf"; +$vcfurl =~ s/\s//g; system ("ln -s $vcfpath $wd/data.vcf"); if (exists($opts{'b'})) { $bamurl = "$dd/data.bam"; + $bamurl =~ s/\s//g; $bamidxurl = "$dd/data.bai"; + $bamidxurl =~ s/\s//g; system ("ln -s $bampath $wd/data.bam"); system ("ln -s $baipath $wd/data.bai"); } |
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| diff -r 04e3bba317f4 -r db44ff975de8 VCF_to_VariantDB.xml --- a/VCF_to_VariantDB.xml Thu Jun 05 04:02:28 2014 -0400 +++ b/VCF_to_VariantDB.xml Tue Jun 10 06:01:18 2014 -0400 |
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| @@ -6,7 +6,7 @@ </macros> <command interpreter="perl"> VCF_to_VariantDB.pl - -H '@URL@' + -H "@URL@" -R $__root_dir__ ## input file -v $input1 |
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| diff -r 04e3bba317f4 -r db44ff975de8 VCF_to_VariantDB_macros.xml --- a/VCF_to_VariantDB_macros.xml Thu Jun 05 04:02:28 2014 -0400 +++ b/VCF_to_VariantDB_macros.xml Tue Jun 10 06:01:18 2014 -0400 |
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| @@ -6,6 +6,6 @@ </requirements> </xml> <token name="@URL@"> - $GALAXY_URL/ + \$GALAXY_URL/ </token> </macros> |