.travis.yml

language: python
python: "3.6"

branches:
    only:
        - beta3
    
os:
 - linux

before_install:
   - sudo apt-get update
   - sudo apt-get install gzip
   - sudo ln -s /bin/tar /bin/gtar # this is because devtools requires gtar which I think is just an alias for 'tar'

install:
   - wget https://repo.continuum.io/miniconda/Miniconda3-4.6.14-Linux-x86_64.sh -O miniconda.sh;
   - bash miniconda.sh -b - p $HOME/miniconda
   - export PATH="$HOME/miniconda/bin:$PATH"
   - hash -r
   - conda config --set always_yes yes --set changeps1 no
   - conda update -q conda
   - conda info -a
   - conda config --add channels defaults
   - conda config --add channels r
   - conda config --add channels conda-forge
   - conda config --add channels bioconda
   - travis_wait conda create -q -n test-environment snakemake r r-devtools perl-app-cpanminus perl=5.26.2=h470a237_0 python=$TRAVIS_PYTHON_VERSION

script:
   - source activate test-environment
   - conda install -c r r-testthat
   - cpanm Bio::Perl
   - cpanm Statistics::Lite
   - Rscript -e 'devtools::install_github("TBradley27/filtar_R")'
   - snakemake --version
   - travis_wait 50 snakemake --use-conda -p results/targets/mmu/oocyte_chrY.contextpp.tsv --config sequence_data_source=SRA conservation=False reannotation=False mirnas="['mmu-miR-188-5p']" transcripts="['ENSMUST00000189888.6']" TPM_expression_threshold=0 prediction_algorithm=TargetScan7 && head results/targets/mmu/oocyte_chrY.contextpp.tsv && rm -f results/targets/mmu/oocyte_chrY.contextpp.tsv ## create empty target for downstream command
   - snakemake --use-conda -p results/targets/miRanda/mmu/oocyte/chrY.tsv --config sequence_data_source=SRA conservation=False reannotation=False mirnas="['mmu-miR-188-5p']" transcripts="['ENSMUST00000189888.6']" TPM_expression_threshold=0 prediction_algorithm=miRanda
   - head results/targets/miRanda/mmu/oocyte/chrY.tsv
   - snakemake --use-conda -p results/targets/mmu/oocyte_chrY.contextpp.tsv --config sequence_data_source=SRA conservation=True reannotation=False mirnas="['mmu-miR-188-5p']" transcripts="['ENSMUST00000189888.6']" TPM_expression_threshold=0 prediction_algorithm=TargetScan7
   - head results/targets/mmu/oocyte_chrY.contextpp.tsv
   - R -e 'test=testthat::test_file("scripts/targetscan_test.R"); stopifnot(test[[1]]$results[[1]]$message=="success")'