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ebi-pf-team / interproscan

Genome-scale protein function classification
Apache License 2.0
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Interest in conda packaging? #95

Closed abretaud closed 2 years ago

abretaud commented 5 years ago

Hi, I'd love to be able to install interproscan using conda, but no package is currently available. Would you be interested if I work on it?

Currently it's not easy to package it because the release archive contains both the code, the dependencies, and the data. It's just not possible to make a 10Gb conda package.

If there could be a minimal release archive containing only the code and the dependencies, we could make a conda package of it and ship a small script to download data from an external archive. Do you think it could be possible?

Ideally, dependencies would not need to be shipped in the minimal tarball if they are available as independent conda packages (like blast).

gsn7 commented 5 years ago

a good start would be to look at the interpro ftp site: each release has an alt directory: ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.34-73.0/alt/

the following files would be of interest: interproscan-core-5.35-74.0.tar.gz
interproscan-data-5.35-74.0.tar.gz

interproscan-core has all the jars and the binary dependencies interproscan-data has all the data required to run interproscan

abretaud commented 5 years ago

Ah cool, I didn't know this was available! What are mgbin and mgdata files? These files are free to redistribute? I'll look into creating a recipe from this.

ropolomx commented 5 years ago

I would be interested as well! Are there any updates on the creation of a bioconda recipe?

abretaud commented 5 years ago

I've looked a little into it, but it's a lot of work. IIRC the core archive comes with precompiled binaries that would not be usable as is (ie would not run on older linux versions as they were compiled on a recent distribution). Each of them would need to be rebuilt in a conda package. I don't have too much time to work on this atm, feel free to work on it if you want!

Juke34 commented 4 years ago

There is plenty of dependencies and they are not yet all into conda:

Once done we can package interproscan

Juke34 commented 4 years ago

Now we have all dependencies I started a recipe you can find here #22802

abretaud commented 4 years ago

That's super cool, thanks a LOT @Juke34 !

drelo commented 3 years ago

Now we have all dependencies I started a recipe you can find here #22802

@Juke34 Hi! Did you managed to make the recipe? Do you have a link?

Juke34 commented 3 years ago

I think I have made something like 90% of the work but I had to drop the project because I have changed job and do not have any time to finish... See discussion here https://github.com/bioconda/bioconda-recipes/issues/21601

drelo commented 3 years ago

Thanks for the response! And this seems like a great ongoing work!

El vie, 15 ene 2021 a las 13:04, Jacques Dainat (notifications@github.com) escribió:

I think I have made something like 90% of the work but I had to drop the project because I have changed job and do not have any time to finish... See discussion here bioconda/bioconda-recipes#21601 https://github.com/bioconda/bioconda-recipes/issues/21601

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