wercker.yml

box: brettbj/continuous_analysis_base
build:
  steps:
    - script:
        name: Run Tests + Coverage
        code: |
          nose2 --plugin nose2.plugins.junitxml --junit-xml test 
          mv nose2-junit.xml wercker/tests.xml
          coverage run --branch test.py
          coverage xml -o wercker/coverage.xml test.py
    
    - script:
        name: Run Kallisto
        code: |
          cd /kallisto/test
          kallisto index -i transcripts.idx transcripts.fasta.gz &>-
          kallisto quant -i transcripts.idx -o output -b 100 reads_1.fastq.gz reads_2.fastq.gz &>-
          cp -R /kallisto/test/output /pipeline/source/wercker/output

    - script:
        name: Plot Results
        code: |
          cd /pipeline/source
          jupyter nbconvert --to html --execute ./Wercker_Plotting.ipynb

    - script:
        name: Push Results back to github
        code: |
          git config user.email "alexwhan@gmail.com"
          git config user.name "Alex Whan"
          git config --global push.default simple
          git remote set-url origin https://alexwhan:$git_publish_key@github.com/alexwhan/continuous_analysis.git

          git checkout master
          git pull
          git add wercker/.
          git commit -a -m "Wercker output [CI SKIP] [SKIP CI] ."
          git stash
          git push