diff --git a/.travis.yml b/.travis.yml new file mode 100644 index 0000000..a002e23 --- /dev/null +++ b/.travis.yml @@ -0,0 +1,38 @@ +sudo: required +lanugage: python +python: + - "2.7" +before_install: + - sudo apt-get update + # Install miniconda. + - if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then + wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh; + else + wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh; + fi + - 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 +install: + - conda create --name phylotyper + - source activate phylotyper + - conda install -c mdwhitesi -c bioconda -c conda-forge -c compbiocore phylotyper + - mkdir out +script: + - phylotyper genome stx1 out example_data/genome.fasta + - phylotyper genome stx2 out example_data/genome.fasta + - phylotyper genome eae out example_data/genome.fasta +after_failure: + # This should not trip after we've update the blast ver. + - conda env export | grep blast + - conda update -c bioconda -c conda-forge -y blast + - conda env export | grep blast + - phylotyper genome stx1 out example_data/genome.fasta + - phylotyper genome stx2 out example_data/genome.fasta + - phylotyper genome eae out example_data/genome.fasta +notifications: + email: false diff --git a/conda/phylotyper/meta.yaml b/conda/phylotyper/meta.yaml index 9088c82..9a74e91 100644 --- a/conda/phylotyper/meta.yaml +++ b/conda/phylotyper/meta.yaml @@ -5,7 +5,7 @@ package: source: fn: master.zip url: https://github.com/superphy/insilico-subtyping/archive/master.zip - # md5: + # md5: # patches: # List any patch files here # - fix.patch @@ -29,7 +29,7 @@ build: requirements: build: - - python + - python - biopython - rpy2 <=2.8 - setuptools @@ -51,13 +51,13 @@ requirements: - r-igraph - bioconductor-biostrings - mafft - - blast 2.6.0 + - blast >= 2.6.0 - fasttree - - trimal + - trimal run: - - python - - biopython + - python + - biopython - rpy2 <=2.8 - setuptools - pytest @@ -78,7 +78,7 @@ requirements: - r-igraph - bioconductor-biostrings - mafft - - blast + - blast >= 2.7.1 - fasttree - trimal