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Apptainer: Difference between revisions
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==Using Conda in Apptainer == <!--T:112--> | ==Using Conda in Apptainer == <!--T:112--> | ||
< | We will preface this tutorial on how to use Conda inside a container with the following '''important notes''': | ||
#Even inside a container, Conda should be used only as a '''last resort'''. Priority should always be given to using [[Modules|modules]] from our [[Available_software|software stack]], and [[Python|wheels]] from our [[Available_Python_wheels|Python wheelhouse]]. These are optimized for our systems and we are better equipped to provide support if you use them. Please contact us if you need a module or a Python package that is not currently available on our systems. | |||
#This tutorial will use the [https://mamba.readthedocs.io/en/latest/user_guide/micromamba.html micromamba] package manager instead of Conda. If you choose to use Conda instead, keep in mind that its use is subject to [https://legal.anaconda.com/policies/en?name=terms-of-service#terms-of-service Anaconda's Terms of Service] and might require a [https://www.anaconda.com/pricing/terms-of-service-faqs commercial license]. | |||
#This tutorial shows how to create a read-only image, i.e., a one-off <tt>.sif</tt> file containing a Conda environment that has everything you need to run your application. We strongly discourage installing software interactively with Conda inside a container and will not show how to do this here. | |||
Creating an Apptainer image and using Conda to install software inside it is a 3-step process. The first step is to create a <tt>.yml</tt> file describing the Conda environment we wish to create inside the container. In the example that follows, we create the file <tt>environment.yml</tt> . This file is where we give our environment a name, then give Conda a list of packages that must be installed and the channels where to look for them. For more information [https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#create-env-file-manually see here]. | |||
{{File | |||
|name=environment.yml | |||
|lang="yaml" | |||
|contents= | |||
name: base | |||
channels: | |||
- conda-forge | |||
- bioconda | |||
- defaults | |||
dependencies: | |||
- python | |||
- pip | |||
- star | |||
- bwa | |||
- multiqc | |||
}} | |||
Second, we create an Apptainer [https://apptainer.org/docs/user/main/definition_files.html image definition file]. This file, here called <tt>image.def</tt>, describes what are the steps Apptainer should take to create our image. These steps are: | |||
#Pull a Docker image from DockerHub that has the micromamba package manager pre-installed. | |||
#Create a copy of the Conda environment definition file <tt>environment.yml</tt> isnide the container | |||
#Call micromamba and have it configure the environment defined in <tt>environment.yml</tt>. | |||
{{File | |||
|name=image.def | |||
|lang="yaml" | |||
|contents= | |||
Bootstrap: docker | |||
From: mambaorg/micromamba:latest | |||
%files | |||
environment.yml /environment.yml | |||
%post | |||
micromamba install -n base --file environment.yml && \ | |||
micromamba clean --all --yes | |||
}} | |||
The last step is to build the Apptainer image using the definition file above: | |||
module load apptainer | |||
APPTAINER_BIND=' ' apptainer build image.sif image.def | |||
==Using Spack in Apptainer == <!--T:114--> | ==Using Spack in Apptainer == <!--T:114--> | ||