From 04f59c5cfe3b19cfd36a87d0697856b091c76dbb Mon Sep 17 00:00:00 2001 From: Kiarod Pashminehazar Date: Tue, 26 Sep 2023 15:29:36 -0700 Subject: [PATCH 1/3] updated SAMTools Version to 1.18 --- CHANGELOG.md | 3 +++ Dockerfile | 2 +- README.md | 2 +- metadata.yaml | 2 +- 4 files changed, 6 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 8cf45ba..d60be79 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,6 +10,9 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm ## [Unreleased] --- +## [1.18] 2023-09-26 +### Changed +- Update SAMTools version to 1.18 ## [1.17] 2023-05-18 ### Changed diff --git a/Dockerfile b/Dockerfile index 85db316..4e25d7b 100644 --- a/Dockerfile +++ b/Dockerfile @@ -3,7 +3,7 @@ ARG MINIFORGE_VERSION=22.9.0-2 FROM condaforge/mambaforge:${MINIFORGE_VERSION} AS builder # Use mamba to install tools and dependencies into /usr/local -ARG SAMTOOLS_VERSION=1.17 +ARG SAMTOOLS_VERSION=1.18 RUN mamba create -qy -p /usr/local \ -c bioconda \ -c conda-forge \ diff --git a/README.md b/README.md index e884fca..11875c9 100644 --- a/README.md +++ b/README.md @@ -9,7 +9,7 @@ SAMtools documentation [here](http://www.htslib.org/doc/samtools.html). # Version | Tool | Version | |------|---------| -|SAMtools| 1.17 | +|SAMtools| 1.18 | --- diff --git a/metadata.yaml b/metadata.yaml index b2550f8..649e2c3 100644 --- a/metadata.yaml +++ b/metadata.yaml @@ -5,7 +5,7 @@ maintainers: ['rhughwhite@mednet.ucla.edu'] contributors: ['Rupert Hugh-White', 'Helena Winata', 'Arpi Beshlikyan', 'Jaron Arbet', 'Sorel Fitz-Gibbon', 'Beth Neilsen'] languages: ['Dockerfile'] tools: ['SAMtools'] -version: ['1.17'] +version: ['1.18'] purpose: 'A tool for reading/writing/editing/indexing/viewing SAM/BAM/CRAM format' references: 'Li H et al. Bioinformatics 25, (2009)' image_name: 'samtools' From ef23c83b61681e63c12b9e879ef7450eeff215b5 Mon Sep 17 00:00:00 2001 From: Kiarod Pashminehazar Date: Tue, 26 Sep 2023 15:32:12 -0700 Subject: [PATCH 2/3] added myself as contributor --- metadata.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/metadata.yaml b/metadata.yaml index 649e2c3..63c707c 100644 --- a/metadata.yaml +++ b/metadata.yaml @@ -2,7 +2,7 @@ category: 'docker' description: 'Docker repository for SAMtools' maintainers: ['rhughwhite@mednet.ucla.edu'] -contributors: ['Rupert Hugh-White', 'Helena Winata', 'Arpi Beshlikyan', 'Jaron Arbet', 'Sorel Fitz-Gibbon', 'Beth Neilsen'] +contributors: ['Rupert Hugh-White', 'Helena Winata', 'Arpi Beshlikyan', 'Jaron Arbet', 'Sorel Fitz-Gibbon', 'Beth Neilsen', 'Kiarod Pashminehazar'] languages: ['Dockerfile'] tools: ['SAMtools'] version: ['1.18'] From a69c32f932b9264001f7193d44748687e10a4059 Mon Sep 17 00:00:00 2001 From: Kiarod Pashminehazar <142354008+kiarod@users.noreply.github.com> Date: Tue, 17 Oct 2023 16:50:03 -0700 Subject: [PATCH 3/3] Update CHANGELOG.md --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index d60be79..317a5fc 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,7 +10,7 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm ## [Unreleased] --- -## [1.18] 2023-09-26 +## [1.18] 2023-10-17 ### Changed - Update SAMTools version to 1.18