bsmn/bsmn-pipeline

identify components that have already been containerized

Closed this issue · 5 comments

kdaily commented
identify components that have already been containerized
kdaily commented

GATK: https://hub.docker.com/r/broadinstitute/gatk/ for the latest version; currently using version 3.7 (https://hub.docker.com/r/broadinstitute/gatk3/ so probably broadinstitute/gatk3:3.7-0)
Picard: currently using 2.12.1 (https://github.com/broadinstitute/picard/releases/tag/2.12.1) but also could use docker broadinstitute/picard

kdaily commented

BWA (current: 0.17.6a; available 0.17.5 at https://hub.docker.com/r/biocontainers/bwa/)

kdaily commented

@sean-cho has contributed quite a few Dockerized tools:

https://github.com/bsmn/pevsnerlab/tree/master/plab_docker/

kdaily commented

migrating this to the common workflow implementation.

https://github.com/bsmn/bsmn-common-workflow/