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Daniel-Liu-c0deb0t / UMICollapse

Accelerating the deduplication and collapsing process for reads with Unique Molecular Identifiers (UMI). Heavily optimized for scalability and orders of magnitude faster than a previous tool.
MIT License
62 stars 8 forks source link

Any chance of making a Conda package? #18

Open CharlotteAnne opened 2 years ago

CharlotteAnne commented 2 years ago

Any chance of packaging this up for Bioconda? would make containerising + Nextflow stuff so much easier!!

Program is working so great I want it in my pipelines!

CharlotteAnne commented 2 years ago

Another thing!! In this same vein it would great if you could add a version argument to the tool so we can version control our pipelines using the tool.

CharlotteAnne commented 1 year ago

Hi - I've gone ahead and make a conda package for UMICollapse >> https://anaconda.org/bioconda/umicollapse users can now install using the command conda install -c bioconda umicollapse. You might want to add this to your documentation. The versioning is pinned to my fork of the repo. Once this propogates to biocontainers, I can also submit the nf-core module to make it easy to use for Nextflow programmers.

Daniel-Liu-c0deb0t commented 1 year ago

Ah thank you so much! (I have not published packages to bioconda before.)

CharlotteAnne commented 1 year ago

No problem, happy to help!

CharlotteAnne commented 1 year ago

just realised there's an issue with the dependencies :// - will try to fix now!!

CharlotteAnne commented 1 year ago

its fixed now, should be working https://anaconda.org/bioconda/umicollapse

CharlotteAnne commented 1 year ago

Hi -- just a nudge, it would be worth adding this as an installation instruction in your readme as it will make things easier for a lot of people. Can be installed to a conda environment with conda install -c bioconda umicollapse

CharlotteAnne commented 1 year ago

the nf-core module is also available and tested >> https://nf-co.re/modules/umicollapse

Daniel-Liu-c0deb0t commented 1 year ago

Sorry for the delay. I've added the conda instructions and the nf-core link to the readme. Thanks for doing this!