Commit 4b30c034 authored by aknecht2's avatar aknecht2
Browse files

Updated example docs.

parent 1507e9ea
Examples
==========
Whenever generating a workflow, there are three required files. A config file,
a run file, and a param file. The config file is used to specify system
information -- paths to required software, environment variables for pegasus
and so on. The run file is used to specify the actual files to process and
what software tools to use on them. Finally, the param file is used to
override any default params for the jobs in the workflow.
**Config**
.. code-block:: yaml
notify:
pegasus_home: "/usr/share/pegasus/"
email: "avi@kurtknecht.com"
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/"
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**
......@@ -51,3 +58,60 @@ Examples
peak: spp
peak_type: narrow
signals: *id003
**Param**
.. code-block:: yaml
macs2_callpeak:
arguments:
"-g": "mm"
bwa_align_single:
arguments:
"-q": 5
"-l": 32
"-k": 2
"-t": 1
bwa_align_paired:
arguments:
"-t": 1
samtools_sam_to_bam:
walltime: 60
memory: 16000
To generate the workflow, pass these input files into the :ref:`chip-gen`
script, like so:
.. code-block:: bash
chip-gen \
--dir DIRECTORY_NAME \
--host DB_HOST \
--username USERNAME \
--password PASSWORD \
--param param.yaml \
--conf config.yaml \
--run run.yaml
This will generate all files necessary to run the workflow in the specified
directory under a date-time stamped folder. The structure will look like this:
.. code-block:: bash
directory_name/
date-timestamp/
input/
chipathlon.dax
conf.rc
db_meta/
notify.sh
sites.xml
submit.sh
output/
work/
From here, you can use the submit.sh script to actually submit the workflow!
submit.sh creates status.sh & remove.sh, which are scripts used to check the
status of the workflow and remove the workflow respectively. Upon completion
of the workflow the notify.sh script is used to email the address specified
in your configuration.
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