Merge pull request #8 from uclahs-cds/bneilsen-Update-To-Use-SAMTools…

…image-base

Update to build on top of samtools docker image

CHANGELOG.md

@@ -9,11 +9,12 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 
 ## [Unreleased]
 
-## [2.2.1_samtools-1.17] - 2023-07-12
+## [2.2.1_samtools-1.17] - 2023-08-08
 ### Changed
 - Updated miniforge to v23.1.0-3
-- Updated SAMTools to v1.17
+- Updated SAMtools to v1.17
 - Updated Dockerfile to meet new lab standards
+- Updated to build on SAMtools docker image as base instead of re-installing SAMtools
 
 ### Added
 - Added autobuild workflow action

Dockerfile

@@ -1,28 +1,21 @@
 ARG MINIFORGE_VERSION=23.1.0-3
+ARG SAMTOOLS_VERSION=1.17
 
 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 \
-    hisat2==${HISAT2_VERSION} \
-    samtools==${SAMTOOLS_VERSION}
+    hisat2==${HISAT2_VERSION}
 
-FROM ubuntu:20.04
+FROM ghcr.io/uclahs-cds/samtools:${SAMTOOLS_VERSION}
 COPY --from=builder /usr/local /usr/local
 
-# 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]>" \ 
+LABEL maintainer="Beth Neilsen <[email protected]>" \
 org.opencontainers.image.source=https://github.com/uclahs-cds/docker-HISAT2