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Christina-hshi / psirc

Full-length linear and circular transcript isoform reconstruction and quantification
MIT License
11 stars 4 forks source link

Prepare for bioconda bundling #7

Open nictru opened 2 months ago

nictru commented 2 months ago

Hello, I am currently working on adding this package to bioconda. It was necessary to fix some problems with current compiler versions as pointed out in #6. Additionally, I removed the local htslib files and instead declared it as an external dependency.

If you are not comfortable with this, I hope we can find a solution - otherwise I can keep building the bioconda package based on my fork

nictru commented 2 months ago

The bioconda PR can be found here. Feel free to add suggestions, in case I got something wrong.

Christina-hshi commented 2 months ago

Hello Nico,

Thanks for adding psirc to bioconda! And also thanks for fixing the issue related to compiler versions! The updates look good to me. I might prefer some tests on my side before merging. Let me know if there is anything that I can help.

Besides, the nf-core/circrna pipeline has a module for BSJ detection, which the psirc method also has. I was wondering whether you are interested in integrating psirc's BSJ detection module as well.

Best, Christina

nictru commented 2 months ago

Hey, as you might have noticed, the bioconda recipe has already been published based on my fork now. Once we can merge this PR, we can of course update the recipe to use the official repo again :) And I am happy that you are planning to test my changes, as I am not much of a C++ programmer myself :D

Yes, I was already thinking about adding the psirc BSJ detection to the pipeline. Also I am planning to add a module for isoform-level detection (and quantification) which will include psirc too. If you want to join the discussion about the development of nf-core/circrna, feel free to join the slack channel :)

Christina-hshi commented 2 months ago

Hi Nico, Sounds great! I will keep you posted. Thanks for inviting me to the slack channel. However, the link didn't work as it said that my email account wasn't tied to the slack channel. Would you mind inviting me via christina.hshi@gmail.com?