biowardrobe-airflow-analysis 1.0.20180430223646

# BioWardrobe backend (airflow+cwl)

### About
Python package to replace [BioWardrobe's](https://github.com/Barski-lab/biowardrobe) python/cron scripts. It uses
[Apache-Airflow](https://github.com/apache/incubator-airflow)
functionality with [CWL v1.0](http://www.commonwl.org/v1.0/).

### Install
1. Add biowardrobe MySQL connection into Airflow connections
```sql
select * from airflow.connection;
insert into airflow.connection values(NULL,'biowardrobe','mysql','localhost','ems','wardrobe','',null,'{"cursor":"dictcursor"}',0,0);
```
2. Install
```sh
sudo pip3 install .
```

### Requirements
1. Make sure your system satisfies the following criteria:
- Ubuntu 16.04.3
- python3.6
```sh
sudo add-apt-repository ppa:jonathonf/python-3.6
sudo apt-get update
sudo apt-get install python3.6
```
- pip3
```sh
curl https://bootstrap.pypa.io/get-pip.py | sudo python3.6
pip3 install --upgrade pip3
```
- setuptools
```sh
pip3 install setuptools
```
- [docker](https://docs.docker.com/engine/installation/linux/docker-ce/ubuntu/)
```sh
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
```sh
sudo apt-get install libmysqlclient-dev
```
- nodejs
```sh
sudo apt-get install nodejs
```
2. Get the latest version of `cwl-airflow-parser`.
If **[Apache-Airflow](https://github.com/apache/incubator-airflow)**
or **[cwltool](http://www.commonwl.org/ "cwltool main page")** aren't installed,
installation will be done automatically with recommended versions. Set `AIRFLOW_HOME` environment
variable to airflow config directory default is `~/airflow/`.
```sh
git clone https://github.com/datirium/cwl-airflow-parser.git
cd cwl-airflow-parser
sudo pip3 install .
```

3. If required, add **[extra airflow packages](https://airflow.incubator.apache.org/installation.html#extra-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:
```sh
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`.
```sh
airflow trigger_dag --conf "{\"job\":$(cat ./hg19.job)}" "bowtie-index"
```
where `hg19.job` is:
```json
{
"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.