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pangenome / pggb

the pangenome graph builder
https://doi.org/10.1101/2023.04.05.535718
MIT License
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vcfwave not found #312

Open aijigekoukou-shen opened 1 year ago

aijigekoukou-shen commented 1 year ago

Hi I downloaded pggb from Conda. I run pggb with the following command: "pggb -i in.fa -o output -n 2 -t 16 -p 90 -s 5000 -V 'PLAS:#:1000'". And I got an error like this: "/home/sparks-fly/biosoft/conda/envs/pggb/bin/time: cannot run vcfwave: No such file or directory Command exited with non-zero status 127". What should I do? Thanks

AndreaGuarracino commented 1 year ago

Currently, pggb on conda is broken, see #294 and https://github.com/bioconda/bioconda-recipes/pull/40520.

About vcfwave, yes, it is still not available on bioconda. We are still not able to build it there, see https://github.com/bioconda/bioconda-recipes/pull/38860, https://github.com/bioconda/bioconda-recipes/pull/40759, https://github.com/bioconda/bioconda-recipes/pull/41003. @pjotrp will help in fixing this. Meanwhile, you could use the docker/singularity flavor of pggb, which is complete and fully updated from yesterday.

aijigekoukou-shen commented 1 year ago

Thanks for your reply. I'll try docker/singularity.