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
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
|
#!/bin/bash
set -e
pkg=bbmap
export LC_ALL=C.UTF-8
if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
# Double quote below to expand the temporary directory variable now versus
# later is on purpose.
# shellcheck disable=SC2064
trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
fi
if ! dpkg-query -s python-biopython-doc | grep -q '^Status: install' >/dev/null
then
cat <<-END
Notice: Please install the python-biopython-doc package to get the
dataset in use by the present test suite.
END
fi
cp -a /usr/share/doc/python-biopython-doc/Tests/Quality/* "${AUTOPKGTEST_TMP}"
cd "${AUTOPKGTEST_TMP}"
set -v
# bbmap
bbmap.sh --version
bbmap.sh --help
bbmap.sh ref=example.fasta
test -d ref
bbmap.sh in=misc_dna_as_sanger.fastq out=out.sam
test -r out.sam
bbmap.sh ref=example.fasta in=example.fastq out=out2.sam nodisk
test -r out2.sam
# bbduk
bbduk.sh --version
bbduk.sh --help
bbduk.sh in1=misc_dna_as_illumina.fastq in2=misc_rna_as_illumina.fastq \
qtrim=rl trimq=15 minlen=75 out=out.fastq.gz
test -r out.fastq.gz
# bbnorm
bbnorm.sh --version
bbnorm.sh --help
bbnorm.sh in=sanger_full_range_original_sanger.fastq qin=33 \
out=out3.fastq outt=outt.fastq hist=hist.plt
test -r out3.fastq
test -r outt.fastq
test -r hist.plt
bbnorm.sh in=illumina_full_range_original_illumina.fastq qin=64 \
out=out4.fastq outt=outt2.fastq hist=hist2.plt
test -r out4.fastq
test -r outt2.fastq
test -r hist2.plt
|
