1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/d161bb983743/ changeset: d161bb983743 user: dan date: 2011-11-08 16:59:27 summary: Squash SAMTools stderr chatter when using FreeBayes which would cause error state. FreeBayes should be updated to e.g. have access to built-in reference genomes, etc. affected #: 1 file diff -r d09e2505fc105eaf9e04c4c973df613f873f6dca -r d161bb98374369c0cc3aa77eed4e162273e64bb3 tools/human_genome_variation/freebayes.xml --- a/tools/human_genome_variation/freebayes.xml +++ b/tools/human_genome_variation/freebayes.xml @@ -5,11 +5,11 @@ </requirements><description>Bayesian genetic variant detector</description><command> - ln -s $reference localref.fa; - ln -s $bamfile localbam.bam; - samtools faidx localref.fa; - samtools sort localbam.bam localbam.bam; - samtools index localbam.bam; + ln -s $reference localref.fa && + ln -s $bamfile localbam.bam && + samtools faidx localref.fa 2>&1 || echo "Error running samtools faidx for FreeBayes" >&2 && + samtools sort localbam.bam localbam.bam 2>&1 || echo "Error running samtools sort for FreeBayes" >&2 && + samtools index localbam.bam 2>&1 || echo "Error running samtools index for FreeBayes" >&2 && freebayes --fasta-reference localref.fa localbam.bam --vcf $output #if $params.source_select == "full": $params.showRefRepeats 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.