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merenlab / anvio

An analysis and visualization platform for 'omics data
http://merenlab.org/software/anvio
GNU General Public License v3.0
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[FEATURE REQUEST] See external/third-party dependencies on program documentation pages #2299

Open ivagljiva opened 1 month ago

ivagljiva commented 1 month ago

A small project to improve anvi'o, based upon feedback/ideas @FlorianTrigodet and I heard from our colleagues at the QIB in Norwich.

The need

We already have a great documentation system integrated into anvi'o that automatically tracks links between programs, artifacts, and workflows. We could extend this system to also keep track of third-party software used within each anvi'o program (for instance, MUSCLE or DIAMOND or Prodigal), so that this information is clearly findable on our help pages (rather than only shown in the occasional CITATION message in terminal output).

The solution

We could add a new type of node in the anvi'o network to represent external dependencies. These could be tracked with something similar to the __requires__ attribute at the top of each program binary, and then automatically parsed into their own section at the top of the program help page.

Beneficiaries

Those who want more transparency about what anvi'o is doing under the hood without actually having to run a program first.

meren commented 1 month ago

We have a similar solution for anvi'o workflows -- see an example here for third-party tools used:

https://anvio.org/help/main/workflows/ecophylo/

Perhaps we can use this mechanism also in programs :)