BioWardrobe backend (airflow+cwl)

About

Python package to replace BioWardrobe's python/cron scripts. It uses Apache-Airflow functionality with CWL v1.0.

Install

1. Add biowardrobe MySQL connection into Airflow connections

   select * from airflow.connection;
   insert into airflow.connection values(NULL,'biowardrobe','mysql','localhost','ems','wardrobe','',null,'{"cursor":"dictcursor"}',0,0);

2. Install

   sudo pip3 install .

Requirements

1. Make sure your system satisfies the following criteria:

   • Ubuntu 16.04.3
     • python3.6

       sudo add-apt-repository ppa:jonathonf/python-3.6
       sudo apt-get update
       sudo apt-get install python3.6

     • pip3

       curl https://bootstrap.pypa.io/get-pip.py | sudo python3.6
       pip3 install --upgrade pip3

     • setuptools

       pip3 install setuptools

     • docker

       sudo apt-get update
       sudo apt-get install apt-transport-https ca-certificates curl software-properties-common
       curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo apt-key add -
       sudo add-apt-repository "deb [arch=amd64] https://download.docker.com/linux/ubuntu $(lsb_release -cs) stable"
       sudo apt-get update
       sudo apt-get install docker-ce
       sudo groupadd docker
       sudo usermod -aG docker $USER

       Log out and log back in so that your group membership is re-evaluated.
     • libmysqlclient-dev

       sudo apt-get install libmysqlclient-dev

     • nodejs

       sudo apt-get install nodejs

2. Get the latest version of cwl-airflow-parser. If Apache-Airflow or cwltool aren't installed, installation will be done automatically with recommended versions. Set AIRFLOW_HOME environment variable to airflow config directory default is ~/airflow/.

   git clone https://github.com/datirium/cwl-airflow-parser.git
   cd cwl-airflow-parser
   sudo pip3 install .

3. If required, add extra airflow packages for extending Airflow functionality, for instance, with MySQL support pip3 install apache-airflow[mysql].

Running

1. To create BioWardrobe's dags run biowardrobe-init in airflow's dags directory

   cd ~/airflow/dags
   ./biowardrobe-init 
   

2. Run Airflow scheduler:

   airflow scheduler

3. Use airflow trigger_dag with input parameter --conf "JSON" where JSON is either job definition or biowardrobe_uid and explicitly specified cwl descriptor dag_id.

   airflow trigger_dag --conf "{\"job\":$(cat ./hg19.job)}" "bowtie-index"

   where hg19.job is:

   {
     "fasta_input_file": {
       "class": "File", 
       "location": "file:///wardrobe/indices/bowtie/hg19/chrM.fa", 
       "format":"http://edamontology.org/format_1929",
       "size": 16909,
       "basename": "chrM.fa",
       "nameroot": "chrM",
       "nameext": ".fa"
     },
     "output_folder": "/wardrobe/indices/bowtie/hg19/",
     "threads": 6,
     "genome": "hg19"
   }

4. All the output will be moved from temporary directory into output_folder parameter of the job.