Getting Started with genomic-config

version: 0.1.7

The genomic-config package provides an interface to configuration files that provide the locations for various genomic based files that might exist on a system. It can be used by external programs and Python code to provide a central point to locate the files. Currently, it only supports ini files but will be expanded to incorporate other configuration file types in the future.

genomic-config provides access to:

1. Reference genome assemblies (fasta files)
2. Reference genotype files (i.e. 1000 genomes)
3. Chain files for liftovers
4. Sample lists
5. variant annotation/mapping VCF files
6. mappings between chromosome synonyms
7. Providing access to a chromosome sort order

There is online documentation.

Installation instructions

Can be installed using either pip or conda.

Using pip:

pip install genomic-config

Using conda:

conda install -c cfin -c bioconda genomic-config

Next steps...

If you have cloned the repository, after installation, you may want to run the tests:

1. Run the tests using pytest ./tests - If you have installed using conda, you will need to clone the repository using git to run the tests.
2. Setup your configuration file.