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OIST's bioinformatics user group Unix goodies images

GitHub actions workflow to create Debian images containing nice Unix tools for OISTs bioinformatics user group.

See also /~https://github.com/oist/BioinfoUgrp and https://salsa.debian.org/plessy/debalamod.

How to use the image on OISTs HPC cluster

  • Activate the modules with ml bioinfo-ugrp-modules UnixGoodies.
  • Discover them with ml av.
  • Load them with ml, followed by the module's name.

How to get the image:

If you are not at OIST or if you need the image elsewhere, you can download it from GitHub with Singularity. If Singularity is available as a module you may need to run ml singularity before pulling the image. Then, pull it with singularity pull docker://ghcr.io/oist/bioinfougrp_unixgoodies_images:latest.

Goodies in this image:

File management

  • archivemount: mounts an archive for access as a file system.
  • duc: file usage analysis (command-line and graphical).
  • duf: filesystem usage/free analysis.
  • gt5: file usage analysis.
  • exa: colorful ls with tree option.
  • ncdu: file usage analysis.
  • rename: use Perl regular expressions to rename files.
  • trash-cli: trashcan system.

File compression

  • grabix: Efficiently extract the n-th line of a bgzip-compressed file.
  • p7-zip: can uncompress and repair some large Zip files that other tools can not.
  • pigz: compress files faster using plenty of CPU cores.
  • pixz: compress files faster using plenty of CPU cores.
  • tabix: provides the bgzip command to produced indexed gzip files.

File transfers

  • filezilla: graphical interface for file transfers.
  • lftp: text interface for file transfers.
  • magic-wormhole: transfer a file to anywhere in the Universe.
  • ncftp: text interface for file transfers.
  • rsync: fast incremental file transfers.

Software development

  • bat: syntax coloring.
  • colordiff: color your diffs.
  • gitk: visualise your Git tree.
  • icdiff: side-to-side color word-diffs.
  • kakoune: modal text editor friently assistant and more.

Other tools

  • cowsay: let the cow say it for you.
  • datamash: command-line tools for computing statistics on numbers from text files.
  • fzf: command-line fuzzy finder.
  • hyperfine: command-line benchmarking tool.
  • libsixel: display images in your terminal!
  • neofetch: System information and OS logo.
  • thef...: swear and the computer fixes your typos.

How to add a goodie to the image

Please open an issue or contact us on our Teams channel.

For admins, how to tag the image

Make sure you have a token with write permissions for packages.

podman login ghcr.io
podman pull  ghcr.io/oist/bioinfougrp_unixgoodies_images:latest
podman tag   ghcr.io/oist/bioinfougrp_unixgoodies_images:latest ghcr.io/oist/bioinfougrp_unixgoodies_images:12.6-2
podman push  ghcr.io/oist/bioinfougrp_unixgoodies_images:12.6-2

For admins, how to create the modules

This is likely to change in the future.

ml singularity
./debalamod.sif cp /debalamod .
for pkg in $(./debalamod.sif cat /debalamod_pkg_list); do ./debalamod $pkg; done

And then module use …

Consider adding at next build

  • tbd…

To be checked after next Debian release