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ngs-fzb / MTBseq_source

MTBseq is an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from illumina whole genome sequence data of Mycobacterium tuberculosis complex isolates.
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installing v1.1.0 #89

Closed peflanag closed 1 year ago

peflanag commented 1 year ago

Hi, I am trying to install on my MacBook Air M2 using iTerm running Rosetta. I have created a Conda env and when I use Conda to install it just hangs. It's been hating for nearly 24hrs now as you can see from the image below. Is there an issue with the Conda install method?

Cheers!

Screenshot 2023-08-18 at 06 52 11
cutpatel commented 1 year ago

Hi, this is usually not a problem of the package itself but of conda and can have multiple reasons. You could first try to update your conda and delete the environment and create it new. Have you setup your channels as recommended by bioconda? You could also try to change channel priority settings: conda config --set channel_priority flexible or conda config --set channel_priority false. You could also try mamba: https://github.com/mamba-org/mamba. I once had success with their not recommended option of installing mamba in the conda base env. I found here many other suggestions to try, maybe the libmamba is a good option: https://bobbyhadz.com/blog/solving-environment-failed-with-initial-frozen-solve-retrying#try-to-set-the-solver-to-libmamba

peflanag commented 1 year ago

Cheers @cutpatel, I will try these and see!

peflanag commented 1 year ago

Just to tag on, the --solver=libmamba worked for anyone else that might be having an issue!

cutpatel commented 1 year ago

Great and thanks for sharing your solution!