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Auto-apptainer

Auto-apptainer is a help tool that can be used to add software to a SD Desktop virtual machine. It utilizes a library of of Apptainer based software contaners, pre-loaded by CSC. You can suggest a container to be added to the library.

Auto apptainer is not available by default, but you must install it first using SD Software installer. After that you can lauch the tool with command:

auto-apptainer
By deafault, this lists all the Apptainer packages available. From the list you can select the backage to be installed.

Alternatively you can add a fltering criteria to the command. In this case only those containers whose name or one of commands that the container provides, matches the search creiteria, are listed.

For example command :

auto-apptainer bam

asks the user to choose from two contaiers: bamtools and bedtools. Bedtools is included as it provides commands bamToBed and bamToFasta that match the serach criteria in this case.

Once a container is selected, one more apptainer warpper based commands are created to drectory: /shared-directory/sd-tools/bin. These commands can mostly be used like natively installed commands. For example after installing the Bamtools container, Bamtools can be startted with command:

bamtools