hpds_geno_load.md

Below are the steps to populate genomic data in HPDS.

Note: Before you begin, please update the PIC-SURE All-In-One Jenkins Server by running git pull then ./update-jenkins.sh in the pic-sure-all-in-one directory on your server. This will build a new Jenkins server image and restart Jenkins with the latest jobs and plugins.

Populate /usr/local/docker-config/vcfLoad with your source data.

In the /usr/local/docker-config/vcfLoad directory, please include the following files:

• vcfIndex.tsv: a file that describes the VCF file(s) to be loaded. Note: For more information about the vcfIndex.tsv format, see https://github.com/hms-dbmi/pic-sure-hpds-genotype-load-example#loading-your-vcf-data-into-hpds.
• vcfLoad/: a directory containing the vcf file(s) that will be read and converted to the hpds format.

Upload Data into HPDS

Load Genomic Data from VCF using the Jenkins job - "Load Genomic Data". To do this, access jenkins on port 8080.

This job loads HPDS data from /usr/local/docker-config/vcfLoad and may take several minutes.