Updating the conda environment

[rajwanir]

Hi @freeseek

Would it be feasible for you to release a new conda version based on the current dev version 1.20? My department uses a SnakeMake wrapper to do some QC analysis and conda seems the most straightforwad way to incorporate gtc2vcf in the pipeline The current conda version lags behind some updates.

Alternatively, I could embed the dev version gtc2vcf.so into the pipeline codebase.

Thank you for your help.

[freeseek]

I am not involved with making conda packages. However, once you install the latest version of BCFtools, you can simply download x86-64 binaries from here

[rajwanir]

Thanks @freeseek. I can incorporate the plugin binary into the pipeline. Just to confirm once no licensing issues in redistributing the gtc2vcf binaries along with our pipeline (https://github.com/NCI-CGR/GwasQcPipeline)? The pipeline is used in different HPC systems by academic groups to QC the infinium genotyping data.

[freeseek]

That's great. You just have to satisfy the MIT license, so you have to keep:

• The original copyright notice
• A copy of the license itself

[rajwanir]

So appending to the pipeline license (https://github.com/NCI-CGR/GwasQcPipeline?tab=MIT-1-ov-file) that "This pipeline includes the bcftools/gtc2vcf binary which is redistributed under the following license: { .. text from https://github.com/freeseek/gtc2vcf?tab=MIT-1-ov-file .. }"

Would this be ok? Thanks.

[freeseek]

See here for an example of how to include multiple licenses into the same LICENSE file

[rajwanir]

Thanks so much @freeseek for sharing the BCFtools example. Based on the example, I have appended the gtc2vcf license here https://github.com/NCI-CGR/GwasQcPipeline/blob/data_catalog/LICENSE and added the pre-compiled binary to the pipeline for user's convenience. Hopefully that resolves it.

Feel free to let me know if anything stands out to you on this.

Thanks for this great tool and being highly responsive for the discussions.