forked from adamewing/bamsurgeon
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy path.travis.yml
80 lines (80 loc) · 3.36 KB
/
.travis.yml
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
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
language: python
dist: precise
python:
- 2.7.8
- 2.7
sudo: required
before_install:
- bash prerequisites.sh
- WORKDIR=`pwd`
- wget https://github.com/broadinstitute/picard/releases/download/1.131/picard-tools-1.131.zip
- unzip picard-tools-1.131.zip
- git clone https://github.com/adamewing/exonerate.git
- cd exonerate
- git checkout v2.4.0
- autoreconf -i
- ./configure --prefix=$WORKDIR && make && make check && make install
- cd ..
- wget https://www.ebi.ac.uk/~zerbino/velvet/velvet_1.2.10.tgz
- tar xvzf velvet_1.2.10.tgz
- sudo make -C velvet_1.2.10
- sudo cp velvet_1.2.10/velvetg $WORKDIR/bin/
- sudo cp velvet_1.2.10/velveth $WORKDIR/bin/
- wget https://github.com/pysam-developers/pysam/archive/9c4c00a22fbf0f836347283cb008dbc9183e5e56.zip
- unzip 9c4c00a22fbf0f836347283cb008dbc9183e5e56.zip
- mv pysam-9c4c00a22fbf0f836347283cb008dbc9183e5e56 pysam
- wget https://github.com/cython/cython/archive/137c064f3b28d4bb59d05a9751f60623f2fc9387.zip
- unzip 137c064f3b28d4bb59d05a9751f60623f2fc9387.zip
- mv cython-137c064f3b28d4bb59d05a9751f60623f2fc9387 cython
- cd cython
- python setup.py install
- cd ../pysam
- python setup.py build
- python setup.py install
- cd ..
- cd test_data
- cd ..
- git clone https://github.com/lh3/bwa.git
- cd bwa
- git checkout v0.7.16
- cd ..
- sudo make -C bwa
- sudo cp bwa/bwa $WORKDIR/bin
- git clone https://github.com/samtools/htslib.git
- cd htslib
- git checkout 1.5
- cd ..
- sudo make -C htslib
- git clone https://github.com/samtools/samtools.git
- cd samtools
- git checkout 1.5
- cd ..
- sudo make -C samtools
- sudo cp samtools/samtools $WORKDIR/bin/
- sudo cp samtools/misc/wgsim $WORKDIR/bin/
- git clone https://github.com/samtools/bcftools.git
- cd bcftools
- git checkout 1.5
- cd ..
- sudo make -C bcftools
- sudo cp bcftools/bcftools $WORKDIR/bin/
- export PATH=$WORKDIR/bin/:$PATH
install: true
script:
- python setup.py install
- cd test
- ./test_snv.sh 10 20 ../test_data/Homo_sapiens_chr22_assembly19.fasta
- ./test_indel.sh 20 ../test_data/Homo_sapiens_chr22_assembly19.fasta
- ./test_snv_alt.sh 15 20 ../test_data/Homo_sapiens_chr22_assembly19.fasta
- ./test_snv_avoid.sh 15 20 ../test_data/Homo_sapiens_chr22_assembly19.fasta
# - ./test_indel_bwamem.sh 10 ../test_data/Homo_sapiens_chr22_assembly19.fasta ../picard-tools-1.131/picard.jar
- ./test_indel_maxdepth.sh 10 ../test_data/Homo_sapiens_chr22_assembly19.fasta
- ./test_indel_minmutreads.sh 10 ../test_data/Homo_sapiens_chr22_assembly19.fasta
- ./test_snv_bwamem.sh 15 20 ../test_data/Homo_sapiens_chr22_assembly19.fasta ../picard-tools-1.131/picard.jar
# - ./test_snv_maxdepth.sh 15 20 ../test_data/Homo_sapiens_chr22_assembly19.fasta
- ./test_snv_minmutreads.sh 15 20 ../test_data/Homo_sapiens_chr22_assembly19.fasta
- ./test_snv_skipmerge.sh 15 20 ../test_data/Homo_sapiens_chr22_assembly19.fasta
# - ./test_snv_tmap.sh 15 20 ../test_data/Homo_sapiens_chr22_assembly19.fasta ../picard-tools-1.131/picard.jar
- ./test_sv.sh 15 ../test_data/Homo_sapiens_chr22_assembly19.fasta
- ./test_sv_bwamem.sh ../test_data/Homo_sapiens_chr22_assembly19.fasta
- ./test_sv_inslib.sh ../test_data/Homo_sapiens_chr22_assembly19.fasta