Hi John and all,
We are running an old version of Galaxy v15.10 and use Pulsar to stage certain
jobs to our hpc cluster. This works great and we love it. However, we have
noticed that for certain tools which require metadata to be staged, although
the metadata file is actually staged, the Galaxy pulsar runner fails to rewrite
the file path for the metadata correctly. Here is an example command from the
latest Freebayes wrappers:
ln -s -f '/cluster/galaxy/pulsar/files/staging/32728/inputs/dataset_54494.dat'
'b_0.bam' && ln -s -f
'/Volumes/ngs/database/files/_metadata_files/002/metadata_2754.dat'
'b_0.bam.bai' && ln -s -f
'/cluster/galaxy/pulsar/files/staging/32728/inputs/dataset_54496.dat' 'b_1.bam'
&& ln -s -f '/Volumes/ngs/database/files/_metadata_files/002/metadata_2755.dat'
'b_1.bam.bai' && samtools view -H b_0.bam | grep "^@SQ" | cut -f 2- | awk '{
gsub("^SN:","",$1); gsub("^LN:","",$2); print $1"\t0\t"$2; }' >>
regions_all.bed && samtools view -H b_1.bam | grep "^@SQ" | cut -f 2- | awk '{
gsub("^SN:","",$1); gsub("^LN:","",$2); print $1"\t0\t"$2; }' >>
regions_all.bed && sort -u regions_all.bed > regions_uniq.bed && mkdir
vcf_output && mkdir failed_alleles && mkdir trace && for i in `cat
regions_uniq.bed | awk '{print $1":"$2".."$3}'`; do echo " freebayes --region
'$i' --bam 'b_0.bam' --bam 'b_1.bam' --fasta-reference
'/cluster/galaxy/indexes/danRer7/sam_index/danRer7.fa' --vcf
'./vcf_output/part_$i.vcf' --standard-filters --min-coverage '3' "; done >
freebayes_commands.sh && cat freebayes_commands.sh | parallel --no-notice -j
${GALAXY_SLOTS:-1} && grep "^#" "./vcf_output/part_$i.vcf" > header.txt && for
i in `cat regions_uniq.bed | awk '{print $1":"$2".."$3}'`; do cat
"./vcf_output/part_$i.vcf" | grep -v "^#" || true ; done | sort -k1,1 -k2,2n
-k5,5 -u | cat header.txt - >
'/cluster/galaxy/pulsar/files/staging/32728/outputs/dataset_54897.dat’
As you can see, the file path for the BAM file is correctly re-written but not
the file path for the bam.bai index, which still has a file path local to
Galaxy.
Has anyone come across this problem before and is there a fix? We are very
hesitant to upgrade our Galaxy server as everything else is working perfectly
for us right now.
Thanks,
Richard
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