Initial Checkin

Author: timeu

.dockerignore

@@ -0,0 +1 @@
+.git

Dockerfile

@@ -0,0 +1,27 @@
+# Dockerfile for pygwas-celery worker
+# Version 0.1
+
+FROM timeu/gwas_base
+MAINTAINER Uemit Seren <uemit.seren@gmail.com>
+
+WORKDIR /conf
+
+# necessary otherwise chown won't work
+RUN mkdir /log && mkdir /DATA mkdir /GENOTYPE
+
+# add celery user and group 
+RUN groupadd -r celery && useradd -r -g celery celery 
+RUN chown celery:celery -R /log /DATA
+
+RUN /env/bin/pip install 'gwaportalpipeline>=0.2.7'
+
+ADD celeryconfig.py /conf/celeryconfig.py
+
+# add colume after chown otherwise it doesnt work
+VOLUME  ["/log","/conf","/DATA","/GENOTYPE"]
+
+USER celery
+
+CMD ["-l","INFO","--logfile","/log/celery.log"]
+
+ENTRYPOINT ["/env/bin/celery","-A", "gwaportalpipeline","worker"]

README.md

@@ -0,0 +1,27 @@
+# timeu/pygwas_celery
+
+[`timeu/pygwas_celery`](https://index.docker.io/u/timeu/pygwas_celery) is a [docker](https://docker.io) image that is based on [`timeu/pygwas`](https://registry.hub.docker.com/u/timeu/gwas_base/) docker image and has [celery](http://www.celeryproject.org/) setup in order to run [PyGWAS](https://github.com/timeu/PyGWAS) as a distributed task.
+
+
+## Usage
+
+
+- RUN with default configuration. Listens to all Queues
+
+        docker run -e "BROKER_URL=amqp://username:pw@BROKER_HOST:5672/VHOST" -e "REST_HOST=http://REST_HOST" -e "REST_USERNAME=USERNAME" -e "REST_PASSWORD=PW" timeu/pygwas_celery
+
+- Pass specific options to celery executable (i.e Queue, concurrency, etc)
+
+        docker run -e "BROKER_URL=amqp://username:pw@BROKER_HOST:5672/VHOST" -e "REST_HOST=http://REST_HOST" -e "REST_USERNAME=USERNAME" -e "REST_PASSWORD=PW" timeu/pygwas_celery -Q gwas.portal.fast
+
+
+## Notes
+
+Following volumes are defined: 
+
+ - /conf .. contains the celeryconfig.py file 
+ - /GWASDATA  .. folder where celery will the input & output files
+ - /GENOTYPE .. folder that contains the genotype data
+
+
+

celeryconfig.py

@@ -0,0 +1,25 @@
+from kombu import Exchange, Queue
+import os
+BROKER_URL = os.environ['CELERY_BROKER']
+CELERY_RESULT_BACKEND = 'rpc'
+CELERY_RESULT_PERSISTENT = True
+CELERY_TASK_SERIALIZER = 'json'
+CELERY_RESULT_SERIALIZER = 'json'
+CELERY_ACCEPT_CONTENT = ['json']
+
+gwas_exchange = Exchange('gwas', type='direct')
+enrichment_exchange = Exchange('enrichment',type='direct')
+
+
+
+CELERY_QUEUES = (
+    Queue('gwas.portal.worker.slow', gwas_exchange, routing_key='gwas.portal.worker.slow'),
+    Queue('gwas.portal.worker.fast', gwas_exchange, routing_key='gwas.portal.worker.fast'),
+    Queue('enrichment',enrichment_exchange,routing_key='enrichment')
+)
+
+   
+CELERY_ROUTES = {
+        'gwaportalpipeline.gwas.run_gwas':{'queue':'gwas.portal.worker.fast'},
+        'gwaportalpipeline.enrichment.candidate_gene_list_enrichment':{'queue':'enrichment'}
+}