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Commit f65dccb0 authored by Brandi Cantarel's avatar Brandi Cantarel
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correct isdocker norm_annot.sh used by pindel

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variants/norm_annot.sh
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...@@ -25,9 +25,11 @@ shift $(($OPTIND -1)) ...@@ -25,9 +25,11 @@ shift $(($OPTIND -1))
baseDir="`dirname \"$0\"`" baseDir="`dirname \"$0\"`"
if [[ -z $isdocker ]] if [[ -z $isdocker ]]
source /etc/profile.d/modules.sh then
module load bedtools/2.26.0 samtools/gcc/1.8 bcftools/gcc/1.8 snpeff/4.3q source /etc/profile.d/modules.sh
module load bedtools/2.26.0 samtools/gcc/1.8 bcftools/gcc/1.8 snpeff/4.3q
fi fi
if [[ -a "${index_path}/genome.fa" ]] if [[ -a "${index_path}/genome.fa" ]]
then then
reffa="${index_path}/genome.fa" reffa="${index_path}/genome.fa"
......
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