Merge pull request #5 from uclahs-cds/bneilsen-Update-To-Use-SAMTools…

…image-base

Update to use samtools images as base image

CHANGELOG.md

@@ -7,13 +7,16 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 
 ---
 ## [Unreleased]
-### Added: 
+
+## [2.2.1_samtools-1.17] - 2023-08-08
+### Added:
 - Added autobuild workflow action
 
 ### Changed:
-- Update SAMTools to v1.17
----
+- Update SAMtools to v1.17
+- Update to use SAMtools Docker Image as base image instead of Ubuntu and installing SAMtools again to improve efficiency
 
+---
 ## [2.2.1] - 2021-07-13
 ### Added
 - Created new repository

Dockerfile

@@ -1,27 +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 BWA_MEM2_VERSION=2.2.1
-ARG SAMTOOLS_VERSION=1.17
+
 RUN mamba create -qy -p /usr/local \
     -c defaults \
     -c bioconda \
     -c conda-forge \
-    bwa-mem2==${BWA_MEM2_VERSION} \
-    samtools==${SAMTOOLS_VERSION}
+    bwa-mem2==${BWA_MEM2_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 <BNeilsen@mednet.ucla.edu>" \ 
+LABEL maintainer="Beth Neilsen <BNeilsen@mednet.ucla.edu>" \
 org.opencontainers.image.source=https://github.com/uclahs-cds/docker-BWA-MEM2