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 Apptainer-based software containers, 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 launch the tool with command:
auto-apptainer
By default, this lists all the Apptainer packages available for auto-apptainer. From the list you can select the package to be installed.
Alternatively you can add a filtering criteria to the command. In this case only those containers whose name or one of commands that the container provides, matches the search criteria, are listed.
For example command:
auto-apptainer bam
asks the user to choose from two containers: bamtools and bedtools. Bedtools is included as it provides commands bamToBed and bamToFasta that match the search criteria in this case.
Once a container is selected, one or more Apptainer wrapper-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 started with command:
bamtools
Below you can find a list of software that can be installed with auto-apptainer. The list can be outdated. You can get an up-to-date
list by running command auto-apptainer in SD Desktop.
- bamtools_2.5.2--hd03093a_1
- bedtools_2.31.0
- deepvariant_1.5.0
- finnish-nertag
- hisat2_2.2.1--h87f3376_5
- regenie_3.0.1
- samtools_1.17-2023-06
- seqtk_v1.3-1-deb_cv1
- stringtie_2.2.0--ha025227_1
- taguette
- vcftools_v0.1.16-1
- vsearch_2.23.0--h6a68c12_0
- weeder_2.0--h9f5acd7_7