Mercurial > repos > dereeper > tassel5
annotate tassel.sh @ 11:75948ef196f9 draft
Uploaded
author | dereeper |
---|---|
date | Wed, 03 Jan 2024 10:22:35 +0000 |
parents | e94b8b64929c |
children | 88ea6f8f664e |
rev | line source |
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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 |