Mercurial > repos > dereeper > tassel5
view tassel.sh @ 5:e94b8b64929c draft
planemo upload commit 9f362f944b3ce480662bec519a3d7c7616454b4c
author | dereeper |
---|---|
date | Fri, 24 Aug 2018 08:33:49 -0400 |
parents | 0eebff4180d9 |
children | 88ea6f8f664e |
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#!/bin/bash analyseType=$1; out1=$2; out2=$3; out3=$4; log1=$5; galaxyOutDir=$6; version=$(java -version 2>&1 | grep version) if [[ ! $version =~ 1.8 ]]; then echo "Java found: $version. Tassel 5.0 requires java 1.8..." >&2 exit 1 fi mkdir $galaxyOutDir # Suppression des 6 premiers arguments de la liste des arguments $@ shift; shift; shift; shift; shift; shift; if [[ $analyseType == glm ]] then run_pipeline.pl $* >> $log1 2>&1 mv "$galaxyOutDir/TASSELGLM1.txt" $out1 if [ $? -gt 0 ] ; then exit 1 ; fi ##check the run of commands mv "$galaxyOutDir/TASSELGLM2.txt" $out2 fi if [[ $analyseType == mlm ]] then run_pipeline.pl $* >> $log1 2>&1 mv "$galaxyOutDir/TASSELMLM1.txt" $out1 if [ $? -gt 0 ] ; then exit 1 ; fi ##check the run of commands mv "$galaxyOutDir/TASSELMLM2.txt" $out2 mv "$galaxyOutDir/TASSELMLM3.txt" $out3 fi if [[ $analyseType == ld ]] then run_pipeline.pl $* >> $log1 2>&1 fi if [[ $analyseType == ck ]] then run_pipeline.pl $* >> $log1 2>&1 mv "$galaxyOutDir/kinship.txt" $out1 if [ $? -gt 0 ] ; then exit 1 ; fi ##check the run of commands fi