v3.0.3

Change to Ubuntu + GenPipes 5

The container in now using Ubuntu 24.04.
GenPipes 5 is now available via the container.
Given that GenPipes 5 is now a PyPi package, the dev usage of the container is for now deprecated.

What's Changed

• Consolidation + removing dev GenPipes as GenPipes 5 is a package by @paulstretenowich in #17
• Debug by @paulstretenowich in #18
• Debug dependency for build-and-push-apptainer + wrong env var for tag name by @paulstretenowich in #19

Full Changelog: v2.1.0...v3.0.3

Docker fix and python 3

This release fix problems with the docker version of the container

If no version of the pipeline is picked, the last genpipes release is still automatically loaded and also the default python of the cvmfs release will be loaded. At release time, python 3.8.5 is the cvmfs default. If genpipes -V 3.X.X is requested, the old python 2.7.14 version is loaded.

adding pigz and imagemagic to the base image

image magic should probably be in the cvmfs part, not the base container, but we will live with it for now...

No fuse premount in singularity version

• singularity uses the --fusemount "container:cvmfs2 <repo> <mountpath>" options to mount cvmfs inside the container.

This is the command that makes GenPipes run in a container:

singularity run --cleanenv -S /var/run/cvmfs -B <host_cache_directory>:/cvmfs-cache \
    --fusemount \
      "container:cvmfs2 cvmfs-config.computecanada.ca /cvmfs/cvmfs-config.computecanada.ca" \
    --fusemount "container:cvmfs2 soft.mugqic /cvmfs/soft.mugqic"   \
    --fusemount "container:cvmfs2 ref.mugqic /cvmfs/ref.mugqic" \
    ${SCRIPTPATH}/images/genpipes.sif

New system witout premount.

Needs recent kernel and singularity >= 3.4

R modules fix

Fix dependency of R on the which command

Pre mount fuse

1.1.0

Use Module 3.2.10

1.0.3

init_genpipes

genpipes, but in a container!

• Uses the parrot from cctools to mount cvmfs files inside the container.
• genpipes.sif is a singularity 3.X image.