Mercurial > repos > dereeper > tassel5
annotate tassel.sh @ 5:e94b8b64929c draft
planemo upload commit 9f362f944b3ce480662bec519a3d7c7616454b4c
| author | dereeper |
|---|---|
| date | Fri, 24 Aug 2018 08:33:49 -0400 |
| parents | 0eebff4180d9 |
| children | 88ea6f8f664e |
| rev | line source |
|---|---|
| 3 | 1 #!/bin/bash |
| 2 | |
| 3 analyseType=$1; | |
| 4 out1=$2; | |
| 5 out2=$3; | |
| 6 out3=$4; | |
| 7 log1=$5; | |
| 8 galaxyOutDir=$6; | |
| 9 | |
| 10 version=$(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 | |
| 15 | |
| 16 mkdir $galaxyOutDir | |
| 17 | |
| 18 # Suppression des 6 premiers arguments de la liste des arguments $@ | |
| 19 shift; shift; shift; shift; shift; shift; | |
| 20 | |
| 21 | |
| 22 if [[ $analyseType == glm ]] | |
| 23 then | |
| 24 run_pipeline.pl $* >> $log1 2>&1 | |
| 25 mv "$galaxyOutDir/TASSELGLM1.txt" $out1 | |
|
5
e94b8b64929c
planemo upload commit 9f362f944b3ce480662bec519a3d7c7616454b4c
dereeper
parents:
3
diff
changeset
|
26 if [ $? -gt 0 ] ; then exit 1 ; fi ##check the run of commands |
| 3 | 27 mv "$galaxyOutDir/TASSELGLM2.txt" $out2 |
| 28 fi | |
| 29 | |
| 30 if [[ $analyseType == mlm ]] | |
| 31 then | |
| 32 run_pipeline.pl $* >> $log1 2>&1 | |
| 33 mv "$galaxyOutDir/TASSELMLM1.txt" $out1 | |
|
5
e94b8b64929c
planemo upload commit 9f362f944b3ce480662bec519a3d7c7616454b4c
dereeper
parents:
3
diff
changeset
|
34 if [ $? -gt 0 ] ; then exit 1 ; fi ##check the run of commands |
| 3 | 35 mv "$galaxyOutDir/TASSELMLM2.txt" $out2 |
| 36 mv "$galaxyOutDir/TASSELMLM3.txt" $out3 | |
| 37 fi | |
| 38 | |
| 39 if [[ $analyseType == ld ]] | |
| 40 then | |
| 41 run_pipeline.pl $* >> $log1 2>&1 | |
| 42 fi | |
| 43 | |
| 44 | |
| 45 if [[ $analyseType == ck ]] | |
| 46 then | |
| 47 run_pipeline.pl $* >> $log1 2>&1 | |
| 48 mv "$galaxyOutDir/kinship.txt" $out1 | |
|
5
e94b8b64929c
planemo upload commit 9f362f944b3ce480662bec519a3d7c7616454b4c
dereeper
parents:
3
diff
changeset
|
49 if [ $? -gt 0 ] ; then exit 1 ; fi ##check the run of commands |
| 3 | 50 fi |