PORI cBioportal

This repository is part of the Platform for Oncogenomic Reporting and Interpretation (PORI).

This python package uses the IPR and GraphKB PORI adaptors to create PORI reports from dumps of cbioportal data.

Getting Started

Install via pip

pip install pori_cbioportal

Download Study Data

Study data should be downloaded from cbioportal, for example

wget https://cbioportal-datahub.s3.amazonaws.com/laml_tcga_pan_can_atlas_2018.tar.gz
tar -xvzf laml_tcga_pan_can_atlas_2018.tar.gz

The folder should have the variant and metadata files, for example

laml_tcga_pan_can_atlas_2018
|-- data_clinical_patient.txt
|-- data_clinical_sample.txt
|-- data_CNA.txt
|-- data_fusions.txt
|-- data_log2CNA.txt
|-- data_mutations_extended.txt
`-- data_RNA_Seq_v2_mRNA_median_all_sample_Zscores.txt

Generate Reports

This is then used to generate individual reports for all patients included in the study. Note to do this you will need access to both a GraphKB server for matching and an IPR server for upload.

pori_cbioportal laml_tcga_pan_can_atlas_2018 \
    --study_id "LAML TCGA" \
    --password $PASSWORD \
    --ipr_url https://YOUR_IPR_API_HOST/api \
    --graphkb_url https://YOUR_GRAPHKB_API_HOST/api

The loader will expect default names for the files but this can be overwritten with the other command line arguments. See the help menu for more options

pori_cbioportal --help

Getting Started (For developers)

Install

clone this repository

git clone ssh://[email protected]:7999/dat/pori_cbioportal.git
cd pori_cbioportal

create a virtual environment

python3 -m venv venv
source venv/bin/activate

install the package and its development dependencies

pip install -e .[dev]

Run the tests

pytest tests

Deployment (Publishing)

Install the deployment dependencies

pip install .[deploy]

Build the distribution files

python setup.py install sdist bdist_wheel

Upload the distibutions to the package server (-r defined in your pypirc)

twine upload -r bcgsc dist/*

Deployment (Scripts)

A buildout config is included by default which will build all console scripts defined in the package.

create a virtual environment and install buildout

python3 -m venv venv
source venv/bin/activate
pip install -U pip setuptools zc.buildout

run buildout

buildout

This will create a directory bin with the executable scripts