Apologies - forgot to change the old subject line - will remail now……

On 13 May 2017, at 12:54, Poole, Richard 
<r.po...@ucl.ac.uk<mailto:r.po...@ucl.ac.uk>> wrote:

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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