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.
• broot: navigate directories, find files, and launch commands.
• duc: file usage analysis (command-line and graphical).
• duf: filesystem usage/free analysis.
• dysk: utility listing your filesystems.
• eza: colorful ls with tree option.
• fd-find: fast and user-friendly alternative to find.
• fdupes: identify duplicate files residing within specified directories.
• gt5: file usage analysis.
• lsix: Shows thumbnails in terminal using sixel graphics.
• 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

• bashbro: A Bash-based web file browser.
• 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.
• git-delta: syntax-highlighting pager for git, diff, and grep output.
• icdiff: side-to-side color word-diffs.
• kakoune: modal text editor friently assistant and more.
• meldmerge: graphical visual diff and merge tool.
• powerline-go: A powerline style prompt for your shell.

Cloud tools

• aws-cli: command-line interaction with the Amazon Web Services.
• cmis-client: command line CMIS client tool.
• rclone: Sync files to cloud storage.

Other tools

• asciinema: Record and share your terminal sessions, the simple way.
• 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.
• glances: An Eye on your system.
• glow: Render markdown on the CLI, with pizzazz!
• hyperfine: command-line benchmarking tool.
• libsixel: display images in your terminal!
• mawk: the AWK found on some minimal footprint containers.
• screenfetch: the bash screenshot information tool.
• terminaltexteffects: inline visual effects in the terminal.
• tmux, with sixel support
• thef...: swear and the computer fixes your typos.
• ugrep: grep with fuzzy search, user interface, etc.

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:13.1-1
podman push  ghcr.io/oist/bioinfougrp_unixgoodies_images:13.1-1

For admins, how to create the modules

This is likely to change in the future.

ml singularity
singularity pull docker://ghcr.io/oist/bioinfougrp_unixgoodies_images:13.1-1
ln -s bioinfougrp_unixgoodies_images_13.1-1.sif ./debalamod.sif
./debalamod.sif cp /debalamod .
for pkg in $(./debalamod.sif cat /debalamod_pkg_list); do ./debalamod $pkg; done

And then module use …

To be added

• …

To be checked after next Debian release

• ble.sh: Bash Line Editor.
• pay-respects, a potential replacement for thef…
• xan