Mercurial > repos > dereeper > tassel5
annotate tassel.sh @ 15:88ea6f8f664e draft
Uploaded
| author | dereeper |
|---|---|
| date | Tue, 16 Jan 2024 10:59:25 +0000 |
| parents | e94b8b64929c |
| children |
| 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 | |
| 12 mkdir $galaxyOutDir | |
| 13 | |
| 14 # Suppression des 6 premiers arguments de la liste des arguments $@ | |
| 15 shift; shift; shift; shift; shift; shift; | |
| 16 | |
| 17 | |
| 18 if [[ $analyseType == glm ]] | |
| 19 then | |
| 20 run_pipeline.pl $* >> $log1 2>&1 | |
| 21 mv "$galaxyOutDir/TASSELGLM1.txt" $out1 | |
|
5
e94b8b64929c
planemo upload commit 9f362f944b3ce480662bec519a3d7c7616454b4c
dereeper
parents:
3
diff
changeset
|
22 if [ $? -gt 0 ] ; then exit 1 ; fi ##check the run of commands |
| 3 | 23 mv "$galaxyOutDir/TASSELGLM2.txt" $out2 |
| 24 fi | |
| 25 | |
| 26 if [[ $analyseType == mlm ]] | |
| 27 then | |
| 28 run_pipeline.pl $* >> $log1 2>&1 | |
| 29 mv "$galaxyOutDir/TASSELMLM1.txt" $out1 | |
|
5
e94b8b64929c
planemo upload commit 9f362f944b3ce480662bec519a3d7c7616454b4c
dereeper
parents:
3
diff
changeset
|
30 if [ $? -gt 0 ] ; then exit 1 ; fi ##check the run of commands |
| 3 | 31 mv "$galaxyOutDir/TASSELMLM2.txt" $out2 |
| 32 mv "$galaxyOutDir/TASSELMLM3.txt" $out3 | |
| 33 fi | |
| 34 | |
| 35 if [[ $analyseType == ld ]] | |
| 36 then | |
| 37 run_pipeline.pl $* >> $log1 2>&1 | |
| 38 fi | |
| 39 | |
| 40 | |
| 41 if [[ $analyseType == ck ]] | |
| 42 then | |
| 43 run_pipeline.pl $* >> $log1 2>&1 | |
| 44 mv "$galaxyOutDir/kinship.txt" $out1 | |
|
5
e94b8b64929c
planemo upload commit 9f362f944b3ce480662bec519a3d7c7616454b4c
dereeper
parents:
3
diff
changeset
|
45 if [ $? -gt 0 ] ; then exit 1 ; fi ##check the run of commands |
| 3 | 46 fi |