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 directory: /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 The list can be outdated.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