From 00eef25ffb166d54a3fef19f42645cca614b3099 Mon Sep 17 00:00:00 2001 From: Tom Whalley Date: Fri, 30 Aug 2024 15:17:33 +0000 Subject: [PATCH] CI --- docker/Dockerfile.tbtamr-0.9.9 | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/docker/Dockerfile.tbtamr-0.9.9 b/docker/Dockerfile.tbtamr-0.9.9 index 0295951..c8c6ccc 100644 --- a/docker/Dockerfile.tbtamr-0.9.9 +++ b/docker/Dockerfile.tbtamr-0.9.9 @@ -1,10 +1,10 @@ -FROM ubuntu:focal +FROM ubuntu:jammy WORKDIR / ENV TMPDIR="/data" # LABEL instructions tag the image with metadata that might be important to the user -LABEL base.image="ubuntu:focal" +LABEL base.image="ubuntu:jammy" LABEL dockerfile.version="0.9.9" LABEL software="tbtamr" LABEL description="The pipeline aligns reads to the H37Rv reference using bowtie2, BWA or minimap2 and then calls variants using bcftools. These variants are then compared to a drug-resistance database." @@ -15,8 +15,9 @@ LABEL maintainer3.email="twhalley93@gmail.com" ENV MAMBA_ROOT_PREFIX="/opt/conda" RUN apt-get update -RUN DEBIAN_FRONTEND=noninteractive apt-get install -y git -RUN DEBIAN_FRONTEND=noninteractive apt-get install -y apt-utils wget bzip2 curl +RUN apt-get install -y git +RUN apt-get install -y apt-utils wget bzip2 curl + RUN curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest| tar -xvj bin/micromamba \ && touch /root/.bashrc \ && ./bin/micromamba shell init -s bash -p /opt/conda \