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.travis.yml
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.travis.yml
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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")'