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BioMuta pipeline

Overview

The BioMuta pipeline gathers mutation data from various sources and combines them into a single dataset under common field structure.

The sources included in BioMuta are:

BioMuta gathers mutation data for the following cancers:

  • DOID:4045 / muscle cancer
  • DOID:10283 / prostate cancer
  • DOID:3565 / meningioma
  • DOID:3277 / thymus cancer
  • DOID:5041 / esophageal cancer
  • DOID:263 / kidney cancer
  • DOID:2394 / ovarian cancer
  • DOID:175 / vascular cancer
  • DOID:9256 / colorectal cancer
  • DOID:4606 / bile duct cancer
  • DOID:11934 / head and neck cancer
  • DOID:2531 / hematologic cancer
  • DOID:1319 / brain cancer
  • DOID:1785 / pituitary cancer
  • DOID:9253 / gastrointestinal stromal tumor
  • DOID:5158 / pleural cancer
  • DOID:184 / bone cancer
  • DOID:1612 / breast cancer
  • DOID:11239 / appendix cancer
  • DOID:1781 / thyroid cancer
  • DOID:2174 / ocular cancer
  • DOID:0060073 / lymphatic system cancer
  • DOID:10534 / stomach cancer
  • DOID:8618 / oral cavity cancer
  • DOID:3953 / adrenal gland cancer
  • DOID:1793 / pancreatic cancer
  • DOID:1192 / peripheral nervous system neoplasm
  • DOID:2998 / testicular cancer
  • DOID:1324 / lung cancer
  • DOID:3121 / gallbladder cancer
  • DOID:4159 / skin cancer
  • DOID:3571 / liver cancer
  • DOID:363 / uterine cancer
  • DOID:3070 / malignant glioma
  • DOID:4362 / cervical cancer
  • DOID:11054 / urinary bladder cancer

Features

BioMuta pipeline comprises two steps:

  1. Download Downloads mutation lists from each source. TBA: cBioPortal fields, cBioPortal studies
  2. Convert Formats all resources to the BioMuta standard for both data and field structure.

Usage

Project Structure

License

Acknowledgements

The liftover from GRCh37 to GRCh38 was performed with the LiftOver command line tool developed by UCSC (insert link).

Setting config parameters

After cloning this repo, you will need to set the parameters given in pipeline/config.json.

Deprecated documentation

Requirements

The following must be available on your server:

  • Node.js and npm
  • docker

Setting config parameters

After cloning this repo, you will need to set the parameters given in cof/config.json. The "server" paramater can be "tst" or "prd" for test or production server respectively. The "app_port" is the port in the host that should map to docker container for the app.

Creating and starting docker container for the APP

From the "app" subdirectory, run the python script given to build and start container:

python3 create_app_container.py -s {DEP}
docker ps --all

The last command should list docker all containers and you should see the container you created "running_hivelab_app_{DEP}". To start this container, the best way is to create a service file (/usr/lib/systemd/system/docker-hivelab-app-{DEP}.service), and place the following content in it.

[Unit]
Description=Glyds APP Container
Requires=docker.service
After=docker.service

[Service]
Restart=always
ExecStart=/usr/bin/docker start -a running_hivelab_app_{DEP}
ExecStop=/usr/bin/docker stop -t 2 running_hivelab_app_{DEP}

[Install]
WantedBy=default.target

This will allow you to start/stop the container with the following commands, and ensure that the container will start on server reboot.

$ sudo systemctl daemon-reload 
$ sudo systemctl enable docker-hivelab-app-{DEP}.service
$ sudo systemctl start docker-hivelab-app-{DEP}.service
$ sudo systemctl stop docker-hivelab-app-{DEP}.service

Mapping APP and API containers to public domains

To map the APP and API containers to public domains (e.g. www.hivelab.org and api.hivelab.org), add apache VirtualHost directives. This VirtualHost directive can be in a new f ile (e.g. /etc/httpd/conf.d/hivelab.conf).

<VirtualHost *:443>
  ServerName www.hivelab.org
  ProxyPass / http://127.0.0.1:{APP_PORT}/
  ProxyPassReverse / http://127.0.0.1:{APP_PORT}/
</VirtualHost>

where {APP_PORT} and {API_PORT} are your port for the APP and API ports in conf/config.json file. You need to restart apache after this changes using the following command:

$ sudo apachectl restart