wercker.yml

box: continuumio/miniconda

# comment
build:
  steps:
    # add github to known hosts
    # see https://github.com/wercker/support/issues/223#issuecomment-223513004
    # see https://github.com/wercker/step-add-to-known_hosts
    - add-to-known_hosts:
        hostname: github.com
        fingerprint: 16:27:ac:a5:76:28:2d:36:63:1b:56:4d:eb:df:a6:48
        type: rsa

    # Build the phylip tools so we can use dnapars.
    # first we need to install the C compiler...
    - install-packages:
        packages: build-essential xvfb FastTree

    # scripts expect fasttree to be in CamelCase.
    - script:
        name: Fixup FastTree
        code: |
          ln -s /usr/bin/fasttree /usr/bin/FastTree

    # download and build phylip sources.
    - script:
        name: Build dnapars
        code: |
          wget http://evolution.gs.washington.edu/phylip/download/phylip-3.696.tar.gz
          tar xzf phylip-3.696.tar.gz && rm phylip-3.696.tar.gz
          make -C phylip-3.696/src -f Makefile.unx install EXEDIR=/usr/bin

    # now install the other python dependencies
    - script:
        name: Install dependencies
        code: |
          conda config --add channels conda-forge 
          conda config --add channels bioconda
          conda install pandas biopython flask nestly pyqt
          conda install pip
          pip install seqmagick
          pip install ete3 scons flask-breadcrumbs

    # fetch a copy of partis; the pipeline references partis files
    # when parsing partis output
    - script:
        name: Install sourcecode dependencies
        code: |
          git clone --depth 1 https://github.com/psathyrella/partis.git
          export PARTIS=$PWD/partis


    # Run Dave's script to parse some sample partis data.
    # The annotation and partition sample data was copied and renamed from
    # in the partis repo.
    # https://github.com/psathyrella/partis/blob/master/test/reference-results/partition-new-simu-cluster-annotations.csv
    # https://github.com/psathyrella/partis/blob/master/test/reference-results/partition-new-simu.csv
    - script:
        name: convert from partis output....
        code: |
          bin/process_partis.py \
             --annotations sampledata/QW333.043-Vk/Hs-LN2-5RACE-IgG-new-cluster-annotations.csv \
             --partition sampledata/QW333.043-Vk/Hs-LN2-5RACE-IgG-new.csv \
             --partis_log sampledata/QW333.043-Vk/test.log \
             --cluster_base cluster \
             --output_dir output_post_partis \
             --separate

    # Run SCons on the output from the previous step
    # The SConstruct script will product files under "output/"
    - script:
        name: run pipeline to prepare data for web site
        code: |
          scons --datapath=output_post_partis

    # The next step if you wanted to seed the output on a web server
    # would be to run the cftweb Flask app,
    # 	cd cftweb && python -m cftweb --file=../output/metadata.json
    
deploy:
  steps:
    # There are no deployment steps yet.  Theoretically you would copy
    # the output to a server that is hosting your web site.