New plugin q2-pear - review and assistance needed


(Ahmed Bassiouni) #1

Dear QIIME2 developers,

I have created a new plugin:
q2-pear

I have submitted it to the q2 library
https://library.qiime2.org/plugins/q2-pear/17/
I still did not make it go live yet.
It is quite basic now.
Future plans include developing join stats csv output – hopefully to be available in the next version – so at least it is on par with the vsearch join-pairs plugin functionality.

It would be great if the qiime2 developers would be able to provide feedback or review of the repo if possible, since I had not released software publicly as such before and I am new to plugin development.

And re declaring it on the qiime2 library : I don’t know how to install it using conda etc (what to put into the install instructions part). Your help would be much appreciated if I want to declare this live on the qiime2 library.

Thank you everyone for developing great open-source software!!

Best Regards,
Ahmed


(Claire Duvallet) #2

Congrats on your first plugin @bassio!!

Before anyone can install your plugin with conda, you need to build it as a conda package. It’s a bit confusing at first, but what this means is that you have to use conda-build to create a .tar.gz file that contains all the instructions for installing your package, and then upload that to anaconda.org so people can download it with ‘conda install’. I wrote a blog post that explains this process, which you can find on the dev docs or my personal website.

Someone else should check me on this, but I think the trickiest part will be getting PEAR itself to be conda-installable. I’m pretty sure that having all dependencies be conda-installed is required to build a package. (Again, someone should double-check that for me). I imagine that this forum post (minus all the metaphlan-specific issues) in combination with my blog post might be enough to get you started?

I’m in thesis-writing mode now, so unfortunately can’t help you with this. If you still haven’t gotten the help you need by the end of January, however, I’d be happy to take a look and provide feedback!


(Jamie Morton) #3

As @cduvallet suggested, the easiest route may to create your own conda channel and upload your binaries there.

If you want to have your recipe hosted on a more publicly available avenue, it maybe worthwhile to checkout conda-forge or bioconda