anvi-draw-kegg-pathways: command not found

[marlaux]

The program anvi-draw-kegg-pathways is not found in my currrent anvi'o installation

Hello guys, first of all thank you very much for this amazing tool, I've been using anvi'o for some months already and I'm positive that I'll continue to use it for a long time. For those that work with metabolic reconstruction, anvi'o came literally as a gift. Just perfect. The unique enzymes feature is... seriously, you rock! Unfurtunetely, The final step to the tip of Everest is not working for me... I checked my installation, everything else is working just fine, but the program anvi-draw-kegg-pathways is "not found". Is there a reason for that? Thank you very much

anvi'o version

anvi-self-test --version

Anvi'o .......................................: marie (v8)
Python .......................................: 3.10.14

Profile database .............................: 38
Contigs database .............................: 21
Pan database .................................: 16
Genome data storage ..........................: 7
Auxiliary data storage .......................: 2
Structure database ...........................: 2
Metabolic modules database ...................: 4
tRNA-seq database ............................: 2

[meren]

Dear @marlaux, I will forward your nice comments to @ivagljiva and @semiller10, and close this issue with a quick and boring response:

The program is only in our anvio-dev branch, and has not yet appeared in a stable version (such as v8). If you were to install anvio-dev (instructions for which are on https://anvio.org/install), you should be able to start using it :)

Best wihses, Meren

[marlaux]

Dear Meren, Thank you, it worked fine using the dev version. I have one question, though If I migrate my dbs to work with the dev version in one directory, the same dbs located in the previous directory, where I was using the stable version, will continue to work fine with the stable version, right? Another question, about the 'collections'. There's some programs which require a collection, but this was the only thing I couldn't quite understand and generate. I am working with MAGs that were already finished. I've created the .db for each one, ran all annotations, profiling, merge profiling, pangenome, phylogenomics, metabolic reconstruction... However, when I try to run, let's say, anvi-split, which requires a collection, I don't have it, or I couldn't create it using the info that I could find throughout the tutorials. I've tried repeatedly, in different ways, I've created the collection info file, no luck at all... Could you help me with this? Thank you very much

Em ter., 24 de set. de 2024 às 09:23, A. Murat Eren (Meren) < @.***> escreveu:

Dear @marlaux https://github.com/marlaux, I will forward your nice comments to @ivagljiva https://github.com/ivagljiva and @semiller10 https://github.com/semiller10, and close this issue with a quick and boring response:

The program is only in our anvio-dev branch, and has not yet appeared in a stable version (such as v8). If you were to install anvio-dev (instructions for which are on https://anvio.org/install), you should be able to start using it :)

Best wihses, Meren

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-- Marcele Laux, PhD Department of Biochemistry, Institute of Chemistry University of São Paulo Omics & Bioinformatics

[semiller10]

Hi @marlaux, you should create copies of the databases before migrating to their latest versions in the dev branch, because the stable and dev codebases can expect different things in databases.

[semiller10]

@marlaux, you can create a collection that contains every item in the database using anvi-script-add-default-collection.