MaAsLin3 conda request

Downstream analysis and statistics
1

Hi all,

Completely understand that this is a tall order, especially for a pre-printed codebase, but I (and I believe the wider community) would really appreciate it if you made MaAsLin3 available via conda.

Thanks!

IZ

2

Hi Zheludev,

Thanks for the suggestion - I’ll take this up with the team. As you probably know, MaAsLin 3 should be available from Bioconductor in the next release, and it’s available from GitHub right now. What would be the advantage to you of installing MaAsLin 3 with Conda provide over installing through R?

Will

3

Hi Will,

I guess there shouldn’t be too big of a difference.

Currently (w/o conda / bioconductor), folks without sudo privileges will struggle because of the harfbuzz / fribidi dependencies…

All the best,

IZ

4

Ah - hopefully once it’s on Bioconductor that’ll be cleared up. If Bioconductor or Conda work equally well, I’ll stick with just Bioconductor then - one less thing to manage. Also, I’m not sure if it helps with the privileges, but you can install from the biobakery division of Bioconductor already:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("biobakery/maaslin3")
5

After a bioconductor releases its easy to create the bioconda release (bioconda-recipes/recipes/bioconductor-maaslin2/meta.yaml at master · bioconda/bioconda-recipes · GitHub). So that would help. The main advantage I see is that bioconda will also create a docker container. We would love to add Maaslin3 to Galaxy, for this we would need the bioconda release as well. Any idea when the bioconductor release is due ? We can work on the bioconda part then.

6

Hi Paul,

Does it specifically need to be a release version or does the current development version on Bioconductor also work? It looks like the next Bioconductor release is in April, and we should be included in that.

If you’re going to add it to Galaxy, would it be better for us to create the bioconda package so that we can keep it up to date?

Will

7

Since bioconductor release is too slow (no offence), I would prefer the current dev version in bioconda, so we can provide an up-to-date interface in Galaxy. We’re happy to help with the recipe, or review it … we will create the Galaxy wrapper as soon as the package is there !

8

Hello Will,

I see there was a discussion here about creating a conda package for MaAsLin3. I kind of want to ask if there was a decision about it and, if not, if it’s possible to create a release on Github to write a recipe.

I will then create the Galaxy wrapper such that MaAsLin3 will be usable in any Galaxy instance. Having a bioconda package makes it easy to maintain since the recipe auto-updates itself if there are no errors. This is only possible when you and your team will still create GitHub releases when there are bigger updates to the software!

It would be nice to hear from you soon about or if there are other ways to make it possible such it can be used for further projects!

Santino