Hi,

We are attempting to integrate vcftools specifically vcf-merge into galaxy. We have two or files that we are attempting to merge, the command when run through terminal does not give a broken pipe, but when galaxy runs the command a broken pipe is given at the beginning and the start of the execution.

The output from the merge appears to be exactly the same. But the broken pipe error causes galaxy to go read on the output wondering if anyone can help that would be much appreciated.

The shell script is pasted below.

_SHELL SCRIPT THAT GALAXY RUNS _ 1 #!/bin/bash 2 # @Date 9/01/2012 3 # @Author Ed Hills, James Boocock 4 # 5 # This file will take a white space separated list of file names, 6 # and run the vcf-merge tool and merge all files into a new file. 7 # 8 # INPUTS 9 # $1 = First input File 10 # $2 = Second input File 11 # $N = Extra input files 12 13 FILE_LIST="" 14 15 cat $1 | bgzip -c > ~tmp1.vcf.gz 16 cat $2 | bgzip -c > ~tmp2.vcf.gz 17 18 tabix -p vcf ~tmp1.vcf.gz 19 tabix -p vcf ~tmp2.vcf.gz 20 21 FILE_LIST="~tmp1.vcf.gz ~tmp2.vcf.gz" 22 23 if [ $# > 2 ] 24 then 25 for ((i=3; i <= $#; i++)) 26 do 27 eval EXTRA_FILE=$${i} 28 cat $EXTRA_FILE | bgzip -c > ~tmp${i}.vcf.gz 29 tabix -p vcf ~tmp${i}.vcf.gz 30 FILE_LIST="${FILE_LIST} ~tmp${i}.vcf.gz" 31 done 32 fi 33 34 perl ~/galaxy-dist/tool-data/shared/vcfperltools/vcf-merge ${FILE_LIST} 2> /dev/null 35 36 rm -f ~tmp* 37

_ERROR MESSAGE_

Warning: The AC tag(s) will not be merged correctly for multiallelic sites. To be handled correctly, please redefine with Number=. or set the environment variable DONT_FIX_VCF40_AG_TAGS=0.

gzip: stdout: Broken pipe Using column name 'HG00096' for ~tmp1.vcf.gz:HG00096 gzip: stdout: Broken pipe Using column name 'NA06986' for ~tmp2.vcf.gz:NA06986

Cheers James.