.travis.yml

language: python
python:
  - "3.6"
  - "3.7"
  - "3.8"

before_install:

  # Here we just install Miniconda, which you shouldn't have to change.

  - wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh
  - chmod +x miniconda.sh
  - ./miniconda.sh -b
  - export PATH=/home/travis/miniconda2/bin:$PATH
  - conda update --yes conda

# command to install dependencies
install:
  - conda create --yes -n uLTRA python=$TRAVIS_PYTHON_VERSION pip 
  - source activate uLTRA
  - pip install ultra-bioinformatics
  - git clone https://github.com/ksahlin/slaMEM.git
  - cd slaMEM
  - make 
  - export PATH=$PATH:$PWD/
  - cd ..
  - git clone https://github.com/lh3/minimap2
  - cd minimap2 && make
  - export PATH=$PATH:$PWD/
  - cd ..
  - wget https://github.com/ksahlin/strobemers/raw/main/strobemers_cpp/binaries/Linux/StrobeMap-0.0.2
  - mv StrobeMap-0.0.2 StrobeMap
  - chmod +x StrobeMap
  - export PATH=$PATH:$PWD/
  - conda install --yes -c bioconda mummer
  #- conda install --yes -c conda-forge -c bioconda medaka openblas==0.3.3 spoa racon minimap2


  # - pip install coveralls
# os:
#   - linux
#   - osx
# safelist
branches:
  only:
  - master
  # - develop
# command to run tests
script: 
      - uLTRA --help
      # - slaMEM
      - uLTRA index test/SIRV_genes.fasta $PWD/test/SIRV_genes_C_170612a.gtf ~/tmp/outfolder/
      # - uLTRA prep_seqs  test/SIRV_genes.fasta ~/tmp/outfolder/ 
      # - slaMEM -l 17 ~/tmp/outfolder/refs_sequences.fa ~/tmp/outfolder/reads_batch_0_rc.fa -o ~/tmp/outfolder/mummer_mems_batch_0_rc.txt
      - uLTRA align test/SIRV_genes.fasta test/reads.fa ~/tmp/outfolder/
      - uLTRA pipeline test/SIRV_genes.fasta $PWD/test/SIRV_genes_C_170612a.gtf test/reads.fa ~/tmp/outfolder/

# after_success: 
#  - coveralls