Merge pull request #31 from uclahs-cds/jsalmingo-update-picard-to-310

Update Picard to 3.10

CHANGELOG.md

@@ -7,7 +7,12 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
 
 This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## ## [Unreleased]
+## [3.1.0] - 2023-09-19
+### Added
+ - Update Picard 3.1.0
+
+### Changed
+ - Use miniforge instead of bl-base
 
 ## [3.0.0] - 2023-03-03
 ### Added

Dockerfile

@@ -1,7 +1,8 @@
-FROM blcdsdockerregistry/bl-base:1.1.0 AS builder
+ARG MINIFORGE_VER=23.3.1-1
+FROM condaforge/mambaforge:${MINIFORGE_VER} AS builder
 
 # Use mamba to install tools and dependencies into /usr/local
-ARG PICARD_VERSION=3.0.0
+ARG PICARD_VERSION=3.1.0
 RUN mamba create -qy -p /usr/local \
     -c bioconda \
     -c conda-forge \
@@ -18,4 +19,5 @@ RUN groupadd -g 500001 bldocker && \
 # Change the default user to bldocker from root
 USER bldocker
 
-LABEL maintainer="Selina Wu <[email protected]>"
+LABEL maintainer="Joseph Salmingo <[email protected]>" \
+      org.opencontainers.image.source=https://github.com/uclahs-cds/docker-Picard

README.md

@@ -4,12 +4,12 @@ UCLA CDS Dockerfile for Picard (picard-slim) from the Broad Institute. A set of
 # Documentation
 
 Picard can be found on GitHub at [broadinstitute/picard](https://github.com/broadinstitute/picard).
-`picard.jar` can be found at `/usr/local/share/picard-slim-3.0.0-0/picard.jar`
+`picard.jar` can be found at `/usr/local/share/picard-slim-3.1.0-0/picard.jar`
 
 # Version
 | Tool | Version |
 |------|---------|
-| picard-slim | 3.0.0 |
+| picard-slim | 3.1.0 |
 | Java | 1.17 |
 
 ## References

metadata.yaml

@@ -2,10 +2,10 @@
 Category: 'docker'
 Description: 'Docker repository for Picard'
 Maintainers: ['[email protected]']
-Contributors: ['Aaron Holmes', 'Helena Winata', 'Jieun Oh', 'Takafumi Yamaguchi', 'Arpi Beshlikyan', 'Selina Wu', 'Beth Neilsen']
+Contributors: ['Aaron Holmes', 'Helena Winata', 'Jieun Oh', 'Takafumi Yamaguchi', 'Arpi Beshlikyan', 'Selina Wu', 'Beth Neilsen', 'Joseph Salmingo']
 Languages: ['Dockerfile']
 Tools: ['Picard']
-Version: ['3.0.0']
+Version: ['3.1.0']
 Purpose: 'A set of tools for manipulating SAM/BAM/CRAM and VCF file formats'
 References: 'https://github.com/broadinstitute/picard'
 image_name: 'picard'