Minimal GPF instance for HG19

Install GPF system

Install GPF from conda

Install GPF from source

1. Clone the source code repository from https://github.com/iossifovlab/gpf/ and switch to gpf directory

2. Setup gpf python environment using conda:

   conda env create --name gpf --file ./environment.yml
   conda env update --name gpf --file ./dev-environment.yml

3. Activate the gpf environment:

   conda activate gpf

Prepare GPF instance config

1. Clone data-hg19-empty instance repository from https://github.com/iossifovlab/data-hg19-empty and switch to data-hg19-empty directory

2. Review the content of gpf_instance.yaml file. It specifies the minimal configuration needed for a GPF instance:

   • reference genome
   • gene models

3. Consider using cache for Genomic Resource Repository. By default the GPF system uses Genomic Resources Repository (GRR) located at https://www.iossifovlab.com/distribution/public/genomic-resources-repository/ without caching resources. You can change this adding following snippet into your gpf_instance.yaml file:

   grr:
       id: "%(instance_id)s"
       type: "url"
       url: "https://www.iossifovlab.com/distribution/public/genomic-resources-repository/"
       cache_dir: "%($HOME)s/grrCache"

   The cache_dir should point to a folder in your local filesystem that is suitable for storing large files.

4. Consider using impala genotype storage. By default the GPF system uses filesystem genotype storage that has limited capabilities. You can switch to using impala genotype storage by adding and adapting the following snippet into your gpf_instance.yaml file:

   genotype_storage:
       default: genotype_impala
   
   storage:
       genotype_impala:
           dir: "%($DAE_DB_DIR)s/work/"
           hdfs:
               base_dir: /user/%(instance_id)s/studies
               host: localhost
               port: 8020
               replication: 1
           impala:
               db: "%(instance_id)s"
               hosts:
               - localhost
               pool_size: 3
               port: 21050
           storage_type: impala

5. When ready with GPF instance configuration adjustments define environment variable DAE_DB_DIR to point to the data-hg19-empty directory:

   export DAE_DB_DIR=<path to data-hg19-empty directory>