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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 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 The list can be outdated.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.

  • allelecount-4.2.1
  • bamtools_2.5.2--hd03093a_1
  • bcftools_1.20
  • bedtools_2.31.0
  • cnvkit-0.9.12
  • deepvariant_1.5.0
  • EIG_8.0.0
  • hisat2_2.2.1--h87f3376_5
  • htseq-2.0.3
  • image-to-text
  • kneaddata-0.12.0
  • kneaddata-0.12.1
  • mpv-0.34.1
  • p7zio
  • pdf2searchablepdf
  • picard
  • python3-for-medimaging
  • samtools_1.17-2023-06
  • seqtk_v1.3-1-deb_cv1
  • stringtie_2.2.0--ha025227_1
  • taguette.info
  • trimgalore-0.6.9
  • vcftools_v0.1.16-1
  • vsearch_2.23.0
  • weeder_2.0--h9f5acd7_7