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Examples
==========

**Config**

.. code-block:: yaml

    notify:
    pegasus_home: "/usr/share/pegasus/"
    email: "avi@kurtknecht.com"
    profile:
    pegasus:
      style: "glite"
    condor:
      grid_resource: "pbs"
      universe: "vanilla"
      batch_queue: "batch"
    env:
      PYTHONPATH: "/home/swanson/aknecht/.conda/envs/ih_env/lib/python2.7/site-packages/"
      PATH: "/home/swanson/aknecht/.conda/envs/ih_env/bin:/bin/:/usr/bin/:/usr/local/bin/"
      PEGASUS_HOME: "/usr/"

**Run**

.. code-block:: yaml

    genomes:
      mm9:
        bowtie2: /work/ladunga/SHARED/mouse/mm9/mm9.genome.fa
        bwa: /work/ladunga/SHARED/mouse/mm9/mm9.genome.fa
        chrom.sizes: /work/ladunga/SHARED/mouse/mm9/mm9.chrom.sizes
    runs:
    - align: bwa
      assembly: mm9
      controls: &id001
      - ENCFF001NIM
      file_type: fastq
      idr: &id002
      - ENCFF001NIP
      - ENCFF001NIS
      peak: spp
      peak_type: narrow
      signals: &id003
      - ENCFF001NIP
      - ENCFF001NIS
    - align: bowtie2
      assembly: mm9
      controls: *id001
      file_type: fastq
      idr: *id002
      peak: spp
      peak_type: narrow
      signals: *id003