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Update Picard to 3.10 #31

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Sep 19, 2023
Merged

Update Picard to 3.10 #31

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4013244
update to picard 3.10
j2salmingo Sep 12, 2023
0133cf5
update changelog
j2salmingo Sep 12, 2023
a1c3ec1
update miniforge version, maintainer
j2salmingo Sep 19, 2023
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7 changes: 6 additions & 1 deletion CHANGELOG.md
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Expand Up @@ -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
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8 changes: 5 additions & 3 deletions Dockerfile
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@@ -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 \
Expand All @@ -18,4 +19,5 @@ RUN groupadd -g 500001 bldocker && \
# Change the default user to bldocker from root
USER bldocker

LABEL maintainer="Selina Wu <selinawu@mednet.ucla.edu>"
LABEL maintainer="Joseph Salmingo <jsalmingo@mednet.ucla.edu>" \
org.opencontainers.image.source=https://github.com/uclahs-cds/docker-Picard
4 changes: 2 additions & 2 deletions README.md
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Expand Up @@ -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
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4 changes: 2 additions & 2 deletions metadata.yaml
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Expand Up @@ -2,10 +2,10 @@
Category: 'docker'
Description: 'Docker repository for Picard'
Maintainers: ['selinawu@mednet.ucla.edu']
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'