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Update Picard to 3.0.0 #24

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Mar 7, 2023
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Update Picard to 3.0.0 #24

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4 changes: 4 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -9,6 +9,10 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm

## ## [Unreleased]

## [3.0.0] - 2023-03-03
### Added
- Update Picard 3.0.0

## [2.27.4] - 2022-08-03
### Added
- Update Picard to 2.27.4
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3 changes: 2 additions & 1 deletion Dockerfile
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@@ -1,9 +1,10 @@
FROM blcdsdockerregistry/bl-base:1.1.0 AS builder

# Use mamba to install tools and dependencies into /usr/local
ARG PICARD_VERSION=2.27.4
ARG PICARD_VERSION=3.0.0
RUN mamba create -qy -p /usr/local \
-c bioconda \
-c conda-forge \
picard-slim==${PICARD_VERSION}

# Deploy the target tools into a base image
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6 changes: 3 additions & 3 deletions README.md
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Expand Up @@ -4,13 +4,13 @@ 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-2.27.4-0/picard.jar`
`picard.jar` can be found at `/usr/local/share/picard-slim-3.0.0/picard.jar`

# Version
| Tool | Version |
|------|---------|
| picard-slim | 2.27.4 |
| Java | 1.8 |
| picard-slim | 3.0.0 |
| Java | 1.17 |

## References

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4 changes: 2 additions & 2 deletions metadata.yaml
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Expand Up @@ -2,9 +2,9 @@
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']
Contributors: ['Aaron Holmes', 'Helena Winata', 'Jieun Oh', 'Takafumi Yamaguchi', 'Arpi Beshlikyan', 'Selina Wu', 'Beth Neilsen']
Languages: ['Dockerfile']
Tools: ['Picard']
Version: ['2.27.4']
Version: ['3.0.0']
Purpose: 'A set of tools for manipulating SAM/BAM/CRAM and VCF file formats'
References: 'https://github.com/broadinstitute/picard'