From 21e9be5e3b23585569eab50a691f2a96219f3eb6 Mon Sep 17 00:00:00 2001 From: Joseph Salmingo Date: Wed, 9 Oct 2024 15:17:26 -0700 Subject: [PATCH 1/2] update picard version to 3.3.0 --- CHANGELOG.md | 4 ++++ Dockerfile | 2 +- README.md | 2 +- metadata.yaml | 2 +- 4 files changed, 7 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index ee8178d..d2f00ac 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,6 +7,10 @@ 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). +## [3.3.0] - 2024-10-09 +### Added + - Update Picard 3.3.0 + ## [3.2.0] - 2024-06-28 ### Added - Update Picard 3.2.0 diff --git a/Dockerfile b/Dockerfile index b00840f..2be7fbc 100644 --- a/Dockerfile +++ b/Dockerfile @@ -2,7 +2,7 @@ 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=3.2.0 +ARG PICARD_VERSION=3.3.0 RUN mamba create -qy -p /usr/local \ -c bioconda \ -c conda-forge \ diff --git a/README.md b/README.md index 15acdab..663aa11 100644 --- a/README.md +++ b/README.md @@ -9,7 +9,7 @@ Picard can be found on GitHub at [broadinstitute/picard](https://github.com/broa # Version | Tool | Version | |------|---------| -| picard-slim | 3.2.0 | +| picard-slim | 3.3.0 | | Java | 1.17 | ## References diff --git a/metadata.yaml b/metadata.yaml index 44f5d45..1f22ce9 100644 --- a/metadata.yaml +++ b/metadata.yaml @@ -5,7 +5,7 @@ Maintainers: ['selinawu@mednet.ucla.edu'] Contributors: ['Aaron Holmes', 'Helena Winata', 'Jieun Oh', 'Takafumi Yamaguchi', 'Arpi Beshlikyan', 'Selina Wu', 'Beth Neilsen', 'Joseph Salmingo'] Languages: ['Dockerfile'] Tools: ['Picard'] -Version: ['3.2.0'] +Version: ['3.3.0'] Purpose: 'A set of tools for manipulating SAM/BAM/CRAM and VCF file formats' References: 'https://github.com/broadinstitute/picard' image_name: 'picard' From 18f8fc650808e243da3de5e6d9dfca37a344421a Mon Sep 17 00:00:00 2001 From: Joseph Salmingo Date: Fri, 11 Oct 2024 20:05:03 -0700 Subject: [PATCH 2/2] update README --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 663aa11..d9f74e9 100644 --- a/README.md +++ b/README.md @@ -4,7 +4,7 @@ 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-3.1.1-0/picard.jar` +`picard.jar` can be found at `/usr/local/share/picard-slim-3.3.0-0/picard.jar` # Version | Tool | Version |