Mercurial > repos > dereeper > tassel5

comparison tassel.sh @ 3:0eebff4180d9 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author dereeper
date Thu, 02 Nov 2017 05:19:30 -0400
parents
children e94b8b64929c
comparison
equal deleted inserted replaced
2:d8a46ae7ee8a 3:0eebff4180d9
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" $out1
26 mv "$galaxyOutDir/TASSELGLM2.txt" $out2
27 fi
28
29 if [[ $analyseType == mlm ]]
30 then
31 run_pipeline.pl $* >> $log1 2>&1
32 mv "$galaxyOutDir/TASSELMLM1.txt" $out1
33 mv "$galaxyOutDir/TASSELMLM2.txt" $out2
34 mv "$galaxyOutDir/TASSELMLM3.txt" $out3
35 fi
36
37 if [[ $analyseType == ld ]]
38 then
39 run_pipeline.pl $* >> $log1 2>&1
40 fi
41
42
43 if [[ $analyseType == ck ]]
44 then
45 run_pipeline.pl $* >> $log1 2>&1
46 mv "$galaxyOutDir/kinship.txt" $out1
47 fi