Update to v2.2.1_samtools-1.17 and add auto build function, update Dockerfile to meet current standards

.github/workflows/Docker-build-release.yaml

@@ -0,0 +1,20 @@
+---
+on:
+  push:
+    branches: ['main']
+    tags: ['v*']
+  release:
+    types: [published]
+
+jobs:
+  build-and-push-image:
+    runs-on: ubuntu-latest
+    name: A job to build and push a docker image
+    permissions:
+      contents: read
+      packages: write
+    steps:
+      - id: build-push
+        uses: uclahs-cds/tool-Docker-action/build-release@latest
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}

CHANGELOG.md

@@ -9,6 +9,15 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 
 ## [Unreleased]
 
+## [2.2.1_samtools-1.17] - 2023-07-12
+### Changed
+- Updated miniforge to v23.1.0-3
+- Updated SAMTools to v1.17
+- Updated Dockerfile to meet new lab standards
+
+### Added
+- Added autobuild workflow action
+
 ---
 ## [2.2.1] - 2021-05-22
 ### Added

Dockerfile

@@ -1,12 +1,28 @@
-FROM blcdsdockerregistry/bl-base:1.0.0 AS builder
+ARG MINIFORGE_VERSION=23.1.0-3
 
-RUN conda create -qy -p /usr/local \
+FROM condaforge/mambaforge:${MINIFORGE_VERSION} AS builder
+
+# add channels in correct order to avoid missing libcrypto dependency
+# https://github.com/bioconda/bioconda-recipes/issues/12100
+ARG HISAT2_VERSION=2.2.1
+ARG SAMTOOLS_VERSION=1.17
+
+RUN mamba create -qy -p /usr/local \
+    -c defaults \
     -c bioconda \
     -c conda-forge \
-    samtools==1.12 \
-    hisat2==2.2.1
+    hisat2==${HISAT2_VERSION} \
+    samtools==${SAMTOOLS_VERSION}
 
 FROM ubuntu:20.04
 COPY --from=builder /usr/local /usr/local
 
-LABEL maintainer="Julie Livingstone <[email protected]>"
+# Add a new user/group called bldocker
+RUN groupadd -g 500001 bldocker && \
+    useradd -r -u 500001 -g bldocker bldocker
+
+# Change the default user to bldocker from root
+USER bldocker
+
+LABEL maintainer="Beth Neilsen <[email protected]>" \ 
+org.opencontainers.image.source=https://github.com/uclahs-cds/docker-HISAT2

README.md

@@ -4,7 +4,7 @@ Dockerfile for HISAT2, which "is a fast and sensitive alignment program for mapp
 SAMtools is also installed for use in the align-RNA and align-DNA pipelines.
 This is because many aligners (e.g. BWA-MEM2 and HISAT2) only support outputting the uncompressed SAM, which causes a burden on the hard disk IO and limits the performace.
 
-The HISAT2 image with SAMtools is located in the Boutros Lab Docker Hub repo: https://hub.docker.com/repository/docker/blcdsdockerregistry/hisat2_samtools-1.12
+The HISAT2 image with SAMtools is located in UCLAHS-CDS GitHub Packages: https://github.com/orgs/uclahs-cds/packages/container/package/hisat2.
 
 # Documentation
 HISAT2 manual is [here](http://daehwankimlab.github.io/hisat2/manual/)
@@ -13,6 +13,7 @@ HISAT2 manual is [here](http://daehwankimlab.github.io/hisat2/manual/)
 | Tool | Version |
 |------|---------|
 | HISAT2 | 2.2.1 |
+| SAMTools| 1.17 |
 
 ---
 

metadata.yaml

@@ -1,11 +1,12 @@
 ---
 Category: 'docker'
 Description: 'Docker repository for the HISAT2 algorithm'
-Maintainers: ['JLivingstone@mednet.ucla.edu']
-Contributors: ['Julie Livingstone']
+Maintainers: ['BNeilsen@mednet.ucla.edu']
+Contributors: ['Julie Livingstone', 'Beth Neilsen']
 Languages: ['Docker', 'bash']
-Tools: ['HISAT2', 'SAMtools v1.12']
+Tools: ['HISAT2', 'SAMtools v1.17']
 Version: ['2.2.1']
 Purpose of tool: 'Algorithm for aligning RNA-Seq data'
 Dependencies: ['Docker']
 References: 'Kim et al, Nature Biotechnology 37 907-915 (2019)'
+image_name: 'hisat2'