add gnuplot for plot-bamstats

CHANGELOG.md

@@ -8,6 +8,8 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 ---
 
 ## [Unreleased]
+### Added
+- Add gnuplot
 
 ---
 ## [1.21] 2024-09-16

Dockerfile

@@ -1,24 +1,25 @@
 ARG MINIFORGE_VERSION=22.9.0-2
-
 FROM condaforge/mambaforge:${MINIFORGE_VERSION} AS builder
-
 # Use mamba to install tools and dependencies into /usr/local
 ARG SAMTOOLS_VERSION=1.21
 RUN mamba create -qy -p /usr/local \
-    -c bioconda \
     -c conda-forge \
+    -c bioconda \
     samtools==${SAMTOOLS_VERSION}
 
 # Deploy the target tools into a base image
 FROM ubuntu:20.04
 COPY --from=builder /usr/local /usr/local
+# Install gnuplot using apt instead of conda
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends gnuplot-nox && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
 
 # 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="Rupert Hugh-White <[email protected]>" \
-org.opencontainers.image.source=https://github.com/uclahs-cds/docker-SAMtools
+org.opencontainers.image.source=https://github.com/uclahs-cds/docker-SAMtools

README.md

@@ -10,7 +10,7 @@ SAMtools documentation [here](http://www.htslib.org/doc/samtools.html).
 | Tool | Version |
 |------|---------|
 |SAMtools| 1.21  |
-
+|gnuplot| 5.4 patchlevel 10 |
 
 ---
 

metadata.yaml

@@ -4,7 +4,7 @@ description: 'Docker repository for SAMtools'
 maintainers: ['[email protected]']
 contributors: ['Rupert Hugh-White', 'Helena Winata', 'Arpi Beshlikyan', 'Jaron Arbet', 'Sorel Fitz-Gibbon', 'Beth Neilsen', 'Kiarod Pashminehazar']
 languages: ['Dockerfile']
-tools: ['SAMtools']
+tools: ['SAMtools', 'gnuplot']
 version: ['1.21']
 purpose: 'A tool for reading/writing/editing/indexing/viewing SAM/BAM/CRAM format'
 references: 'Li H et al. Bioinformatics 25, (2009)'