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.