gdc-client and MAF-LIB python modules

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This short tutorial is for the end users to install gdc-client and MAF-LIB Python modules on a Conda environment.

The gdc-client is a command-line tool used to interact with the Genomic Data Commons (GDC) API, which is a repository for cancer genomic data managed by the National Cancer Institute (NCI). This tool allows users to download large-scale genomic datasets, such as those from The Cancer Genome Atlas (TCGA).

MAF-LIB is a Python library used to work with Mutation Annotation Format (MAF) files, which are widely used in cancer genomics to store somatic mutations detected in tumor samples. The MAF-LIB module provides tools for parsing, analyzing, and manipulating MAF files, which are essential in understanding cancer mutations and their potential clinical implications.

mkdir gdc-client
cd gdc-client/
wget https://github.com/NCI-GDC/gdc-client/archive/refs/heads/develop.zip
unzip develop.zip
module load python
python -m venv gdc-client-env
source gdc-client-env/bin/activate
pip install -r requirements.txt

modify the setup.py:

#    use_scm_version={"local_scheme": "dirty-tag",},
SETUPTOOLS_SCM_PRETEND_VERSION=1,

Install the gdc-client

python setup.py install
pip install -r dev-requirements.txt

Testing:

python -m pytest tests/
python -m pytest --cov=gdc_client --cov-branch --cov-report term tests/

MAF-LIB:

git clone https://github.com/NCI-GDC/maf-lib.git
cd maf-lib/
pip install -r requirements.txt

Author: Serdar Acir