-
Notifications
You must be signed in to change notification settings - Fork 1
/
.travis.yml
35 lines (35 loc) · 2.23 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
sudo: required
language: python
python:
- "3.6"
install:
- sudo apt-get update -qq
- sudo apt-get install -qq tar python3 bzip2 build-essential
- wget -q https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh
- bash ~/miniconda.sh -b -p /home/travis/miniconda
- /home/travis/miniconda/bin/conda config --set always_yes yes --set changeps1 no
- /home/travis/miniconda/bin/conda update -q conda
- /home/travis/miniconda/bin/conda info -a
- /home/travis/miniconda/bin/conda install scipy numpy pandas git
- /home/travis/miniconda/bin/conda install -c biocore mafft psipred=4.01
- /home/travis/miniconda/bin/conda install -c bioconda clustalo
- /home/travis/miniconda/bin/pip install --upgrade
- /home/travis/miniconda/bin/pip install py pytest pytest-xdist pytest-cov pytest-colordots
- /home/travis/miniconda/bin/pip install biopython python-coveralls buddysuite dill
- /home/travis/miniconda/bin/git clone https://github.com/biologyguy/BuddySuite.git /home/travis/build/biologyguy/BuddySuite
- /home/travis/miniconda/bin/git --git-dir=/home/travis/build/biologyguy/BuddySuite/.git --work-tree=/home/travis/build/biologyguy/BuddySuite checkout develop
- mv /home/travis/build/biologyguy/BuddySuite/buddysuite/*.py /home/travis/miniconda/lib/python3.6/site-packages/buddysuite/
- touch /home/travis/build/biologyguy/RD-MCL/rdmcl/config.ini
- mkdir /home/travis/build/biologyguy/RD-MCL/rdmcl/psipred/
- cp -r /home/travis/miniconda/share/psipred_4.01/data /home/travis/build/biologyguy/RD-MCL/rdmcl/psipred/
- wget -q http://eddylab.org/software/hmmer3/3.1b2/hmmer-3.1b2.tar.gz -O ~/hmmer-3.1b2.tar.gz
- tar -xzf ~/hmmer-3.1b2.tar.gz -C ~/
- sed -i -e 's/p7_gmx_Dump(stdout, fwd, p7_DEFAULT);//g' ~/hmmer-3.1b2/src/generic_fwdback.c
- (cd ~/hmmer-3.1b2 && ./configure && make)
- mv ~/hmmer-3.1b2/src/hmmbuild /home/travis/miniconda/bin/hmmbuild
- (cd ~/hmmer-3.1b2/src && make generic_fwdback_example)
- mkdir /home/travis/build/biologyguy/RD-MCL/rdmcl/hmmer
- cp ~/hmmer-3.1b2/src/generic_fwdback_example /home/travis/build/biologyguy/RD-MCL/rdmcl/hmmer/hmm_fwd_back
- cp ~/hmmer-3.1b2/src/generic_fwdback_example /home/travis/miniconda/bin/hmm_fwd_back
script:
- travis_wait 40 source test.sh