updated samtools to v1.12 (#2)

uclahs-cds · Jul 13, 2021 · bdb7abe · bdb7abe
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -15,3 +15,4 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 ### Added
 - Created new repository
 - Added copied Dockerfile from pipeline-align-DNA
+- Updated SAMtools to v1.12
diff --git a/Dockerfile b/Dockerfile
@@ -5,7 +5,7 @@ LABEL maintainer="Yash Patel <YashPatel@mednet.ucla.edu>"
 # add channels in correct order to avoid missing libcrypto dependency
 # https://github.com/bioconda/bioconda-recipes/issues/12100
 ARG BWA_MEM2_VERSION=2.2.1
-ARG SAMTOOLS_VERSION=1.10
+ARG SAMTOOLS_VERSION=1.12
 RUN conda create -qy -p /usr/local \
  -c defaults \
  -c bioconda \

diff --git a/README.md b/README.md
@@ -1,7 +1,7 @@
 # docker-BWA-MEM2
 Dockerfile for BWA-MEM2 (for mapping DNA sequences against a large reference genome) and SAMtools (for interacting with high-thouroughput sequencing data) used for pipeline-align-DNA.
 
-The current BWA-MEM2 image with SAMtools is located in the Boutros Lab Docker Hub repo: https://hub.docker.com/repository/docker/blcdsdockerregistry/align-dna:bwa-mem2-2.2.1_samtools-1.10. Future updated images will be hosted in separate Boutros Lab Docker Hub repos.
+The current BWA-MEM2 image with SAMtools is located in the Boutros Lab Docker Hub repo: https://hub.docker.com/repository/docker/blcdsdockerregistry/bwa-mem2_samtools-1.12.
 
 # Documentation
 Documentation for BWA-MEM2 can be found here: https://github.com/bwa-mem2/bwa-mem2. Documentation for SAMtools: http://www.htslib.org/doc/.
@@ -10,7 +10,7 @@ Documentation for BWA-MEM2 can be found here: https://github.com/bwa-mem2/bwa-me
 | Tool | Version |
 |------|---------|
 |BWA-MEM2|2.2.1|
-|SAMtools|1.10|
+|SAMtools|1.12|
 
 ---
 

diff --git a/metadata.yaml b/metadata.yaml
@@ -4,7 +4,7 @@ Description: 'Docker repository for BWA-MEM2 and SAMtools'
 Maintainers: ['YashPatel@mednet.ucla.edu']
 Contributors: ['Yash Patel', 'Chenghao Zhu', 'Benjamin Carlin', 'Aakarsh Anand']
 Languages: ['Dockerfile']
-Tools: ['BWA-MEM2', 'SAMtools v1.10']
+Tools: ['BWA-MEM2', 'SAMtools v1.12']
 Version: ['2.2.1']
 Purpose of tool: 'Software packages for mapping DNA sequences against a large reference genome and interacting with high-thouroughput sequencing data'
 References: 'https://github.com/bwa-mem2/bwa-mem2;http://www.htslib.org'