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 the current version of BioMuta are:

• cBioPortal

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.

Installation

1. Clone the Repository:

git clone https://github.com/GW-HIVE/biomuta-old.git

2. Set Up a Virtual Environment (Optional):

While in the root directory, run source env/bin/activate.

3. Install Dependencies: (to be implemented)

pip3 install -r requirements.txt

Configuration

Before running the scripts, please modify the paths in the config.json file to match your local machine setup. The file contains important directory paths used by the scripts, including paths for downloading data, storing results, and other resources.

1. Open the config.json file located in the root of the repository.
2. Modify the following fields to point to the correct directories on your machine:
   • "downloads": Path to the directory where raw data will be saved.
   • "generated_datasets": Path to the directory where processed datasets will be stored.
   • "mapping": Path to the directory containing mapping files. You will only need to modify the path to the root directory since mapping files are already included in the repository.

Example config.json:

{
  "downloads": "/path/to/downloads",
  "generated_datasets": "/path/to/generated_datasets",
  "mapping": "/root/pipeline/convert_step2/mapping"
}

Usage

Step 1: Download

1. Go to pipeline/download_step1/cbioportal

Script execution order (some scripts will be moved into appropriate directories later) 1 - fetch_mutations.sh 2 - cancer_types.py | integrate_cancer_types.sh

UniProt Accession Numbers

1. Extract GRCh37 chromosomic positions and write out in BED format.

• script: /pipeline/convert_step2/liftover/1_chr_pos_to_bed.py
• output: /biomuta/generated/datasets/2024_10_22/liftover/hg19positions.bed

2. Use UCSC LiftOver to convert to GRCh38 chromosomic positions.
   1. Run 2_liftover.sh on hg19positions.bed with the chain file ucscHg19ToHg38.over.chain. You will get successfully mapped positions in hg38positions.bed and unmapped positions in unmapped.bed.
   2. grep -v '^#' unmapped.bed > unmapped_ucsc.bed to delete comments generated by liftOver.
   3. Run the same script but use unmapped.bed as the input and ensembl_GRCh37_to_GRCh38.chain as the chain file. You will get successfully mapped positions in hg38positions_unmapped_by_uscs.bed and unmapped positions in unmapped_ensembl.bed.
3. Grab the corresponding ENSEMBL transcript ID.
   1. For every chromosomal position in the input BED file, in which transcript does it fall? See which range each position falls into in the gff3 file. Grab the corresponding ENSP.
4. Map to ENSEMBL protein ID.
5. Map to UniProt Canonical Accession Numbers.

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