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comparison tassel/tassel.sh @ 2:d8a46ae7ee8a draft

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author dereeper
date Fri, 03 Jul 2015 04:37:26 -0400
parents 0aeea77b924a
children
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1:1dc58d808e72 2:d8a46ae7ee8a
5 out2=$3; 5 out2=$3;
6 out3=$4; 6 out3=$4;
7 log1=$5; 7 log1=$5;
8 galaxyOutDir=$6; 8 galaxyOutDir=$6;
9 9
10 version=$(java -version 2>&1 | grep version)
11 if [[ ! $version =~ 1.8 ]]; then
12 echo "Java found: $version. Tassel 5.0 requires java 1.8..." >&2
13 exit 1
14 fi
10 15
11 mkdir $galaxyOutDir 16 mkdir $galaxyOutDir
12 17
13 # Suppression des 6 premiers arguments de la liste des arguments $@ 18 # Suppression des 6 premiers arguments de la liste des arguments $@
14 shift; shift; shift; shift; shift; shift; 19 shift; shift; shift; shift; shift; shift;
20
15 21
16 if [[ $analyseType == glm ]] 22 if [[ $analyseType == glm ]]
17 then 23 then
18 run_pipeline.pl $* >> $log1 2>&1 24 run_pipeline.pl $* >> $log1 2>&1
19 mv "$galaxyOutDir/TASSELGLM1.txt" $out1 25 mv "$galaxyOutDir/TASSELGLM1.txt" $out1