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Software on TransitΒΆ

Update: 15.12.2025

Transit is an UPPMAX service that can be used to securely transfer files.

The purpose of the transit server is to give users access to their wharf folders on Bianca/Maya on Linux running machine with certain limitations.

  • Users home folders are ephemeral, i.e. any changes will be lost 5 minutes after last interactive login session. The writable portion of the home folder is limited to 2.9GB which could lead to unexpected results when tools need to cache in their usual location (pip, conda, etc).

    df -h | grep $USER
overlay             2.9G  2.4G  580M  81% /gorilla/home/XXXXX

  • X11 and any port forwarding is disabled i.e. graphical tools do not work.

  • Currently, the software module system is not available on transit.
  • Apptainer is available but users needs to redirect TMP and CACHE to their wharf folders. This solution leads to EXTREMELY slow builds. Pulling containers is not affected - it is as fast as saving to wharf.
export APPTAINER_CACHEDIR=$HOME/sens2023531/APPTAINER_CACHE
export APPTAINER_TMPDIR=$HOME/sens2023531/APPTAINER_TMP
mkdir -p $APPTAINER_CACHEDIR $APPTAINER_TMPDIR

Below are some temporary solutions for commonly used tools. Please, use the full path to run the tools.

  • nextflow - /sw/generic/pixi-tools/bin/nextflow
  • nf-core - /sw/generic/pixi-tools/bin/nf-core
  • dds-cli - /sw/generic/uv-tools/tool_bin/dds
  • pyega3 - /sw/generic/uv-tools/tool_bin/pyega3
  • globus-cli - /sw/generic/pixi-tools/bin/globus
  • google-cloud-sdk - /sw/generic/pixi-tools/bin/gcloud,gsutil...
  • ena-webin-cli - /sw/generic/pixi-tools/bin/ena-webin-cli
  • aspera-cli - /sw/generic/pixi-tools/bin/ascli
  • awscli - /sw/generic/pixi-tools/bin/aws