The Genotype and Phenotype in Families (GPF) system manages large databases of genetic variants and phenotypic measurements obtained from collections of families and individual family members.
The main application of the system has been in managing the data gathered from the Simons Simplex Collection, a collection of ~2,600 families with one child diagnosed with autism.
Information on how to use GPF can be found in the GPF documentation.
We recommend using Anaconda environment](https://www.anaconda.com/) for creation of GPF development environment.
Create a conda gpf environment with all of the conda package dependencies
from environment.yml and dev-environment.yml files. From gpf root
directory run:
mamba env create --name gpf --file ./environment.yml
mamba env update --name gpf --file ./dev-environment.ymlTo use this environment, you need to activate it using the following command:
conda activate gpfThe following commands are going to install GPF dae`` and wdae`` packages for
development usage. (You need to install GPF packages in the development gpf
conda environment.)
for d in dae wdae dae_conftests; do (cd $d; pip install -e .); doneThere are some additional genotype storages that are not included in the default GPF installation and if you plan to use or develop features for these genotype storages you need to install their dependencies.
To use ore develop features for GPF impala genotype storage you need some
additional dependencies installed. From gpf root directory update your gpf
conda environment using:
mamba env update --name gpf --file ./impala_storage/impala-environment.ymland install the gpf_impala_storage package using:
pip install -e impala_storageIf you want support for genotype storage on Google Cloud Platform (GCP) using the Google BigQuery for querying variants you need to install more dependencies in your development environment:
mamba env update --name gpf --file ./gcp_storage/gcp-environment.ymland install gcp_genotype_storage package using:
pip install -e gcp_storageTo run the tests you need to authenticate for seqpipe-gcp-storage-testing
project:
gcloud config list project[core]
project = seqpipe-gcp-storage-testing
Your active configuration is: [default]
using
gcloud auth application-default loginTo run the GCP storge tests you should enter into the
gpf/gcp_storage directory and run:
py.test -v gcp_storage/tests/To run the intergration tests use:
py.test -v ../dae/tests/ gcp_storage/tests/gpf_storage.yaml
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