diff --git a/.travis.yml b/.travis.yml deleted file mode 100644 index a97ef36..0000000 --- a/.travis.yml +++ /dev/null @@ -1,29 +0,0 @@ -language: python -python: - # We don't actually use the Travis Python, but this keeps it organized. - - "3.6" - -install: - - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh; - - bash miniconda.sh -b -p $HOME/miniconda - - export PATH="$HOME/miniconda/bin:$PATH" - - hash -r - - conda config --set always_yes yes --set changeps1 no - - conda update -q conda - # Useful for debugging any issues with conda - - conda info -a - - conda config --add channels defaults - - conda config --add channels conda-forge - - conda config --add channels bioconda - - conda create -q -n snakemake snakemake>=5.1.2 python=$TRAVIS_PYTHON_VERSION - - conda create -q -n star star=2.5.3a - - source activate star - # create STAR index (too big to live in git) - - mkdir .test/data/ref/index - - STAR --runMode genomeGenerate --genomeDir .test/data/ref/index --genomeFastaFiles .test/data/ref/genome.chr21.fa - -script: - - source activate snakemake - # run the workflow - - snakemake --use-conda --directory .test || (for f in .test/logs/*; do echo $f; cat $f; done; for f in .test/logs/*/*; do echo $f; cat $f; done; exit 1) - - snakemake --use-conda --use-singularity --directory .test