ResFinder tool to Galaxy

[Jeevan Karloss]

Hi, We are wondering if you are working on having ResFinder in Galaxy toolshed? 1000s of galaxy installations in University and institutions across the world are using Galaxy for analysis. We are also doing the same. Thats why I am asking.

[CGE Helpdesk]

Dear Jeevan Karloss,

Thank you for your interest in ResFinder and your proposal and will consider it. We are currently working on making ResFinder and other services available for Bioconda.

Best,
Karen

[Jeevan Karloss]

Thanks. Is there any timeline regarding the Bioconda thing?

[CGE Helpdesk]

Unfortunately, I cannot guarantee when ResFinder will be available for Bioconda. I can inform you that ResFinder recipe is currently in the making and we do it as quickly as possible. We can let you know once it is ready.

Best,
Karen

[Jeevan Karloss]

Thanks. I (NVI, Oslo) am planning to develop the galaxy wrapper for ResFinder. Would you be interested to collaborate or something? Is there an email address or contact person that. I can contact if I have some questions.

[CGE Helpdesk]

Thanks for reaching out. CGE could be interested in collaborating on a galaxy wrapper for ResFinder. Please send an email to [e-mail] summarizing the idea and issue #58, and I will forward it to the relevant persons.

Best,
Karen

[Jeevan Karloss]

I have sent the email now. Does this code include PointFinder also like the online one?

[CGE Helpdesk]

Dear Jeevan,

Thank you for the email.

Regarding your question, I am not entirely sure I understand it correctly. With code you mean if this repository also holds the code for PointFinder? If this is the case the answer is yes. You can find the two respecitive scripts here: resfinder/cge/pointfinder.py and resfinder/cge/resfinder.py

Best,
Karen, CGE Helpdesk

[Peter Cock]

Is there any work in progress for the bioconda packaging? Galaxy uses conda and bioconda for its dependencies, but this would be worthwhile in its own right - I was hoping to install ResFinder straight from conda too.

I have found https://github.com/bioconda/bioconda-recipes/blob/master/recipes/kma/meta.yaml so at least dependency kma is already done. That was a community packaging contribution back in Dec 2018.

[Peter Cock]

Also done, back in July 2019, is cgecore:
https://github.com/bioconda/bioconda-recipes/blob/master/recipes/cgecore/meta.yaml

I’ve not looked at version numbers, but things look good in terms of the software dependencies (databases are another matter):

$ conda install install blast kma tabulate biopython cgecore gitpython python-dateutil

I think that’s all the dependencies as per https://bitbucket.org/genomicepidemiology/resfinder/src/master/ readily installed from conda (using bioconda and conda-forge).

[CGE Helpdesk]

Dear Peter,

Thank you for the interest. We are currently working on implementing some of our services in Bioconda yes, and ResFinder is a high priority. I unfortunately cannot say when it will be ready.

Thank you for the information about the dependencies, this will for sure make it easier to implement the ResFinder, when these are already available.

Kind regards

Malene, CGE Helpdesk

[RolfKaas]

ResFinder is now available for Bioconda.

However it should be noted that ResFinder only officially releases on bitbucket, pypi, dockerhub, and as a webtool.

All other releases like the bioconda releases are not official releases and are maintained by volunteers from their respective community. We unfortunately do not have the resources to support additional releases.

With that said, we are very willing to help volunteers that want to create and/or maintain ResFinder releases for other platforms and frameworks.