OptiType/.travis.yml at master · elitap/OptiType · GitHub

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sudo: false
language: python
python:
  - "2.7"
addons:
  apt:
    sources:
      - ubuntu-toolchain-r-test
    packages:
      - glpk

before_script:
- wget http://packages.seqan.de/razers3/razers3-3.4.0-Linux-x86_64.tar.bz2
- tar xf razers3-3.4.0-Linux-x86_64.tar.bz2
- pip install numpy
- pip install pyomo
- pip install pysam
- pip install matplotlib
- wget http://www.hdfgroup.org/ftp/HDF5/current/bin/linux-centos7-x86_64-gcc483/hdf5-1.8.16-linux-centos7-x86_64-gcc483-shared.tar.gz
- tar xf hdf5-1.8.16-linux-centos7-x86_64-gcc483-shared.tar.gz
- export LD_LIBRARY_PATH=/home/travis/build/FRED-2/OptiType/hdf5-1.8.16-linux-centos7-x86_64-gcc483-shared/lib:$LD_LIBRARY_PATH
- export HDF5_DIR=/home/travis/build/FRED-2/OptiType/hdf5-1.8.16-linux-centos7-x86_64-gcc483-shared/
- pip install tables
- pip install pandas
script:
  python OptiTypePipeline.py -i ./test/rna/CRC_81_N_2_fished.fastq --rna -v -o ./test/rna/ -c ./test/test_config.ini