conda installations

[Gavin Douglas]

Hi there,

Thanks a lot for developing the placement tools, I think they will be really useful for the field. Does your team have any plans to make conda installation recipes for these tools? I am working on updates to the tool PICRUSt (https://github.com/picrust/picrust2) and currently I am using PaPaRa and EPA-NG for phylogenetic placement (and gappa seems like a useful update for guppy tog). I was thinking of making conda recipes for all 3 tools and uploading them to bioconda, which would make setting up the placement pipeline straight-forward for users. If you're not currently planning to write these recipes yourself would you be against me having a go at it?

Best,

Gavin

[Alexandros Stamatakis]

Dear Gavin,

Thanks a lot for developing the placement tools, I think they will be really useful for the field.

Thank you

Does your team have any plans to make conda installation recipes for these tools?

Not at present.

I am working on updates to the tool PICRUSt (https://github.com/picrust/picrust2) and currently I am using PaPaRa and EPA-NG for phylogenetic placement (and gappa seems like a useful update for guppy tog). I was thinking of making conda recipes for all 3 tools and uploading them to bioconda, which would make setting up the placement pipeline straight-forward for users. If you're not currently planning to write these recipes yourself would you be against me having a go at it?

In principle I am in favor of this, but maybe wait for Lucas and Pierre to also reply who are the main developers of GAPPA and EPA-NG, respectively.

However, please implement a mechanism such that the core computational tools on which picrust2 relies are properly cited along with picrust.

Looking at the original picrust page at:

http://picrust.github.io/picrust/

you do have a link to:

"Additional citation resources: here"

but I believe that this should be on that same page and be more cmandatory, e.g., "users must also cite the tools incorporated into picrust".

This is a common problem when core computational tools are incorporated into pipelines, i.e., only the pipeline is cited, which does not reward all the effort that went into the 3rd party pipeline component development. So please do your best to ensure that the pipeline components get also properly cited.

Thanks a lot,

Alexis 

[Lucas Czech]

Hi Gavin,

thanks for your interest in our tools! Indeed, we are not planning to make them available via conda (as of now) . Of course we would appreciate your efforts, and could maybe link to it from our Readme docs (unless Pierre does not want this for EPA).

As for the citation issue that Alexis mentioned: we are currently working on an application note for genesis and gappa. Once that is available (preprint), please add this to the list of papers that have to be cited as well. I'll let you know here.

There is one caveat though: all our tools are quite young and in active development. Hence, changes in the interface might occur. In particular, gappa will see some changes and added features in the next few weeks.

So long
Lucas

[Gavin Douglas]

Thanks for getting back to me Alexis and Lucas,

I'll take a look at making these conda recipes in the next couple of weeks and let you know once I have working versions (unless I hear otherwise regarding EPA-NG).

I agree that not citing core computational tools is a major issue in bioinformatics - I'll make it clear that these tools needs to be cited as well and I'll keep an eye out for that application note.

Best,

Gavin

[Alexandros Stamatakis]

Dear Gavin,

> Thanks for getting back to me Alexis and Lucas,

> 

> I'll take a look at making these conda recipes in the next couple of 

> weeks and let you know once I have working versions (unless I hear 

> otherwise regarding EPA-NG).

Thanks a lot. 

> I agree that not citing core computational tools is a major issue in 

> bioinformatics - I'll make it clear that these tools needs to be cited 

> as well and I'll keep an eye out for that application note.

Thank you :-) 

Alexis 

[Pierre Barbera]

Hi Gavin,

sounds great! Zero objections from my side, the easier to install the better. EPA-ng should also remain pretty stable in terms of it's interface, as I believe it should be feature-complete for the most part.

Thank you for your efforts!

Pierre

[Gavin Douglas]

Just a quick note that I finally got around to adding EPA-NG to bioconda and it can now be installed with the command "conda install -c bioconda epa-ng".

There is an issue with GAPPA that is causing a bioconda build error, which I posted as an issue on the GAPPA github.

Best,

Gavin

[Pierre Barbera]

Hi Gavin,

many thanks! I've added a note to the README.

Cheers,

Pierre

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[Lucas Czech]

Hi Gavin,

thanks for reporting this. I posted an update on the gappa issues page, see there for details.

Lucas