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A new request to upload a container to <quay.io> h...
# request-core
r
A new request to upload a container to quay.io has been made! • Container URL: docker.io/nourmahfel1/str-ont • Why is this needed?: This is a forked repository from straglr that has been adapted for nanopore data analysis. There is not a docker image for this version. Thank you • Confirmation: ◦ This can't be done through the usual Bioconda Note: only containers with a stable version will be accepted (ie. not 
latest
) Core team will add this container to quay.io. Please react to the message with ✅ when this is done. [This process is not automated] submitter: @Nour Mahfel
✅ 1
n
This tool is based on a fork of straglr that has been adapted for Oxford Nanopore data analysis (epi2me version). While a personal Docker image exists, this version of straglr is not available through bioconda.
Hi, I just wanted to expand on this. Straglr is a tool used for short tandem repeat analysis in long-read sequencing data. The original repository is available here: https://github.com/bcgsc/straglr, and the version I am using is a fork that has been adapted for Nanopore data: https://github.com/philres/straglr. Would it be possible to upload the forked version to quay? Thank you ☺️
👀 1
m
there's pip install for it
is is there not possible to make a seqera container for it?
You seem to only have a 
latest
tag in https://hub.docker.com/r/nourmahfel1/str-ont/tags
Note: only containers with a stable version will be accepted (ie. not 
latest
)
n
Hi Maxime, thank you for letting me know, I will make sure to change the tag to a stable version. I will update you when it is done. I tried to create a seqera container, but only the bioconda version came up, not the forked version. I also tried to use wave cli, but It did not work either.
m
I'll have a look at it locally
❤️ 1
j
Thanks for taking this over @Maxime Garcia!
Yes, I would say this should be on conda, if it's on pip
Or rather your fork should go into bioconda, given it's python should be quite straight forward
You would just need to rename it fo bioconda
e.g. maybe 
straglr-genotype
or 
straglr-ont
or something
Yeah the original straglr is already on bioconda: https://bioconda.github.io/recipes/straglr/README.html
m
Oh so one could install it via pip, but it's not on pip
j
I don't think it is on pip
(the new one)
You can just install it with pip using a remote URL
m
yeah, that mis-lead me
j
So @Nour Mahfel for this you will want to make a bioconda recipe for straglr-genotype (leave an issue on the repo notifiying you are doing it), and it should be quite easy as you can copy most of the existing 
environment.yaml
into the recipe
Fortunately a couple of years ago I wrote a tutorial for bioconda on how to do it 🙂
n
Perfect thank you so much both I will look into this. Would it be ok to do this if the straglr-ont differs from straglr-genotype?
j
Depends on what you mean ?>
n
The fork includes changes to the source code to adapt the tool for nanopore data analysis. The changes were made by epi2me developers, so it is not identical to the original straglr-genotype tool
j
Ok wait, I'm lost now 😆
m
yeah for me this is a fork of a tool, so straglr-ont would be a new one
I'd say go for it
add to bioconda, and from there you can create a seqera container
👍 1
j
We need to see the source code/repo to double check it's OK to do so (but like Maxime says, and according to the license I iamgine it's OK)
❤️ 1
m
I haven't managed to do it locally BTW, so I'm afraid that's the best solution
👍 1
j
It could be epi2me might be OK doing teh bioconda packaiging for you
If there is a request
n
I don't think there is a request, but I will contact them. I will also look into adding it as a new tool to bioconda then will try and create a seqera container for it. Thank you 🙂
🎉 1
m
I am classifying this request as done then as it's a won't do in the end
👍 2
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