1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4f7b7e4ca213/ Changeset: 4f7b7e4ca213 User: dannon Date: 2013-06-21 20:55:12 Summary: Add more package requirements for datatype converters Affected #: 3 files diff -r b31177004e80656b8efdb553291244b2a3e53d6f -r 4f7b7e4ca213498824d5fba7526676ddf976b823 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 @@ -1,5 +1,9 @@ <tool id="CONVERTER_bed_gff_or_vcf_to_bigwig_0" name="Convert BED, GFF, or VCF to BigWig" version="1.0.0" hidden="true"><!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> --> + <requirements> + <requirement type="package">ucsc_tools</requirement> + <requirement type="package">bedtools</requirement> + </requirements><command> ## Remove comments and sort by chromosome. grep -v '^#' $input | sort -k1,1 | diff -r b31177004e80656b8efdb553291244b2a3e53d6f -r 4f7b7e4ca213498824d5fba7526676ddf976b823 lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml --- a/lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml +++ b/lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml @@ -1,6 +1,10 @@ <tool id="CONVERTER_interval_to_bigwig_0" name="Convert Genomic Intervals To Coverage"><!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> --><!-- Used on the metadata edit page. --> + <requirements> + <requirement type="package">ucsc_tools</requirement> + <requirement type="package">bedtools</requirement> + </requirements><command> ## Remove comments and sort by chromosome. diff -r b31177004e80656b8efdb553291244b2a3e53d6f -r 4f7b7e4ca213498824d5fba7526676ddf976b823 lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml --- a/lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml +++ b/lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml @@ -1,4 +1,9 @@ <tool id="CONVERTER_sam_to_bigwig_0" name="Convert SAM to BigWig" version="1.0.0" hidden="true"> + <requirements> + <requirement type="package">ucsc_tools</requirement> + <requirement type="package">samtools</requirement> + <requirement type="package">bedtools</requirement> + </requirements><command> samtools view -bh $input | bedtools genomecov -bg -split -ibam stdin -g $chromInfo 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.