language: python
python: 2.7
os:
  - linux

before_install:
  - curl http://repo.continuum.io/miniconda/Miniconda-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
  - conda info -a

install:
  - conda install -c bioconda humann2
  - conda install -c bioconda goatools

script:
  - ./group_humann2_uniref_abundances_to_GO.sh -i "test-data/humann2_gene_families.csv" -a "test-data/go_02_22_2016.obo" -s "test-data/goslim_metagenomics_02_22_2016.obo" -u "test-data/map_infogo1000_uniref50_02_22_2016.txt" -g `which map_to_slim.py | xargs -n1 dirname` -p `which humann2 | xargs -n1 dirname` -m "test-data/molecular_function_abundances.txt" -b "test-data/biological_process_abundance.txt" -c "test-data/cellular_component_abundance.txt"
  - diff "test-data/molecular_function_abundances.txt" "test-data/expected_molecular_function_abundances.txt"
  - diff "test-data/biological_process_abundance.txt" "test-data/expected_biological_process_abundance.txt"
  - diff "test-data/cellular_component_abundance.txt" "test-data/expected_cellular_component_abundance.txt"