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mzapatka / p-dip

Pathogen discovery pipeline (p-dip)
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issues with installation #1

Open shwetha141 opened 3 months ago

shwetha141 commented 3 months ago

Hello , I am not able to install all the tools for the environment. PackagesNotFoundError: The following packages are not available from current channels:

is there a work around. Should I install it directly from source as trinity ( i think they have removed it from biocinda)

mzapatka commented 3 months ago

Dear #shwetha141,

Could you please try building the environment with micromamba (https://mamba.readthedocs.io/en/latest/installation/micromamba-installation.html)

micromamba env create -n pdip --file pdip.yaml as of today, a build is still successful.

Best regards, Marc

shwetha141 commented 3 months ago

Thank you, it didn't work, since micromamba didn't support most of the packages on the yaml. I changed the trinity specs in the yaml (removed the version number), so now that is working. Now for mbuffer, i tried but it gives me the same error with mamba. I tried compiling it but since, I am running on Mac OS , I don;t think it works, based on the link below.

https://github.com/szaydel/mbuffer