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hsigeman / findZX

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Failed to open source file https://github.com/snakemake/snakemake-wrappers/raw/0.74.0/bio/multiqc/environment.yaml #7

Open zhuangfjnu opened 2 years ago

zhuangfjnu commented 2 years ago

This problem caused by the The Snakemake Wrappers repository https://snakemake-wrappers.readthedocs.io/en/stable/ Soluton:

  1. download this https://github.com/snakemake/snakemake-wrappers/raw/0.74.0/bio/multiqc/environment.yaml file into local. 2,Edit the ./workflow/rules/mapping.smk , ref.smk , trimming.smk , variant_calling_platypus.smk , qc.smk , assembly.smk change the "wrapper:" section like "file://./findZX/multiqc"

I spent 3 days to figure out how to solve this problem!!!!

Zhen

zhuangfjnu commented 2 years ago

You also need to download the wrapper.py file in the https://github.com/snakemake/snakemake-wrappers/tree/0.74.0/bio/fastqc

hsigeman commented 2 years ago

Hi Zhen,

Thank you for the suggested solution. Yes, the problem seem to be related to the Snakemake Wrapper Repository. I decided to replace the MultiQC wrapper with the bioconda version (https://anaconda.org/bioconda/multiqc), which has worked for me and several other users. It's not a perfect fix since it is recommended to use the wrappers when you can, but I'd rather stick with it for now until the wrapper is working again.

Did the updated version of findZX not work for you?

Hanna

zhuangfjnu commented 2 years ago

HI Hanna, I change the multiqc into 1.10.1 in the yaml file, but fail the installation with mamba. I think replace the MultiQC wrapper with the bioconda version is a good idea!

Regards, Zhen

zhuangfjnu commented 2 years ago

which has worked for me and several other users.

It is not work for the users in china. lol