1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b8d8f81bed87/ Changeset: b8d8f81bed87 User: jgoecks Date: 2013-09-25 20:45:25 Summary: For bed/gff/vcf converter, only use -split option when appropriate. Affected #: 1 file diff -r ff806b8e5f18791641fa49a20d9bea9e65215310 -r b8d8f81bed872e58b4691643de8a08fa41662e71 lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml --- a/lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml +++ b/lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml @@ -9,7 +9,12 @@ grep -v '^#' $input | sort -k1,1 | ## Generate coverage bedgraph. - bedtools genomecov -bg -split -i stdin -g $chromInfo + bedtools genomecov -bg -i stdin -g $chromInfo + + ## Only use split option for bed and gff/gff3/gtf. + #if $input.ext in [ 'bed', 'gff', 'gff3', 'gtf' ]: + -split + #end if ## Streaming the bedgraph file to wigToBigWig is fast but very memory intensive; hence, this ## should only be used on systems with large RAM. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.