Rewrite of Scicommander in Go with much improved algorithm

Tue, 03 Sep 2024 11:15:02 +0200

When I presented a poster about SciCommander at the Swedish bioinformatics workshop last year, I got a lot of awesome feedback from some great people including Fredrik Boulund, Johannes Alneberg and others, of which I unfortunately lost the names (please shout out if you read this!).

(For those new to SciCommander, it is my attempt at creating a tool that can track complete provenance reports also for ad-hoc shell commands, not just those included in a pipeline. The grand plan is also to integrate this provenance tracking with those of popular pipelines, to enable seamless provenance report generation across pipelines and ad-hoc commands).

SciCommander - track provenance of any shell command

Thu, 09 Nov 2023 18:38:00 +0100

I haven’t written much about a new tool I’ve been working on in some extra time: SciCommander .

I just presented a poster about it at the Swedish Bioinformatics Workshop 2023 , so perhaps let me first present you the poster instead of re-iterating what it is (click to view large version):

New version not requiring running the scicmd command

I got a lot of great feedback from numerous people at the conference, most of who pointed out that it would be great if one could start scicommander as a kind of subshell, inside which one can run commands as usual, instead of running them via the scicmd -c command.

Scicommander on Living Systems_

Rewrite of Scicommander in Go with much improved algorithm

SciCommander - track provenance of any shell command

New version not requiring running the scicmd command