diff --git a/apptainer/apptainer.qmd b/apptainer/apptainer.qmd index 14a40ae..b301379 100644 --- a/apptainer/apptainer.qmd +++ b/apptainer/apptainer.qmd @@ -5,7 +5,7 @@ Lesson plan based around materials from [CodeRefinery](https://coderefinery.gith ## What are containers? - Containers isolate software, dependencies, configurations, and system libraries from the host system -- The naming came from the idea of shipping containers (which are portable & standardized) +- The naming came from shipping containers (which are portable & standardized) - Virtual machines are a similar concept, but these virtualise hardware, contain complete operating systems (including the kernel), and are managed by software known as a hypervisor - Containers on the other hand share the host OS kernel, so they don't contain complete operating systems, just user space system libraries - This makes them lightweight, portable, and fast to start up @@ -56,18 +56,18 @@ Bootstrap: docker From: debian:12.5-slim %environment - export PATH=$PATH:/root/.pixi/bin + export PATH=$PATH:/root/.pixi/bin %runscript - cat /etc/debian_version + cat /etc/debian_version %post - export PATH=$PATH:/root/.pixi/bin - apt-get update && \ - apt-get install -y curl && \ - curl -fsSL https://pixi.sh/install.sh | bash && \ - apt-get clean && \ - pixi global install -c bioconda -c conda-forge minigraph + export PATH=$PATH:/root/.pixi/bin + apt-get update && \ + apt-get install -y curl && \ + curl -fsSL https://pixi.sh/install.sh | bash && \ + apt-get clean && \ + pixi global install -c bioconda -c conda-forge minigraph ``` @@ -113,7 +113,7 @@ From: debian:12.5-slim - Once built, images are hosted by AWS and can be pulled by anyone (will last at least 5 years from creation) - Seqera pays for the build compute, hosting of the containers is by Seqera on AWS and paid for by AWS donated credits - To pull the built container: -`aapptainer pull oras://community.wave.seqera.io/library/bwa_minigraph_pixi:c4c589e18eae6698` +`apptainer pull oras://community.wave.seqera.io/library/bwa_minigraph_pixi:c4c589e18eae6698` ``` bwa