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ParkinsonLab / MetaPro

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bwa, faidx command not found #19

Closed rishidash12 closed 10 months ago

rishidash12 commented 10 months ago

Based on Metapro tutorial while indexing ChocoPhlAn database for BWA and DIAMOND getting error bwa and faidx command not found.

billytaj commented 10 months ago

what's the command you typed? Sounds like the command is wrong, or docker/singularity wasn't installed correctly. Not a MetaPro issue.

rishidash12 commented 10 months ago

this is below command i have used bwa index -a bwtsw - samtools faidx i put chocophlan path as well.

billytaj commented 10 months ago

You're not invoking any of the docker/singularity image. Metapro doesn't install these tools for you. We package it inside a container.

You need to use singularity/docker. Please take another look at our documentation, and perhaps the tutorial too.

Please also consult the documentation docker/singularity provide.

rishidash12 commented 9 months ago

Can you please guide me how to invoke because I am new to docker. I followed each step in metapro tutorial.

billytaj commented 9 months ago

This level of support is beyond my capacity to provide. I suggest that you contact a more senior bioinformatician at your institution or signup for the Canadian Bioinformatics workshop https://bioinformatics.ca/