1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
|
#!/bin/sh -e
pkgname=optimir
if [ "$AUTOPKGTEST_TMP" = "" ] ; then
AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkgname}-test.XXXXXX`
trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
fi
cd $AUTOPKGTEST_TMP
cp -a /usr/share/doc/${pkgname}/examples/* $AUTOPKGTEST_TMP
DIR_OUT=results
VCF=genotypes.vcf
# Example 1
optimir process \
--fq S1.fq.gz \
--vcf genotypes.vcf
# Example all
optimir libprep \
-v $VCF \
-o $DIR_OUT
optimir process \
--fq S1.fq.gz \
--vcf $VCF \
--gff_out \
--dirOutput $DIR_OUT
optimir process \
--fq S2.fq.gz \
--vcf $VCF \
--gff_out \
--dirOutput $DIR_OUT
# Make summary files
optimir summarize \
--dir $DIR_OUT/OptimiR_Results
|
