CODEWITHSUNDEEP
pythoncondaubuntu-20.04mamba
Chooseel Bunsuwansakul
Chooseel Bunsuwansakul

Reputation: 61

conda and mamba were broken (segmentation fault) after installing "conda install -c asmeurer glibc"

I am a Thai microbiologist try to use command line. I installed "Ubuntu 20.04 on Windows" then bowtie2 by conda:

conda install -c bioconda bowtie2

and then check version of the bowtie2. it is 2.2.5 but I need 2.4.5. the con labels is weird like this https://github.com/BenLangmead/bowtie2/issues/397 but that is not the main point.

I try everything on the Internet. finally, it worked on MacOX somehow.

but for "Ubuntu 20.04 on Windows" because bowtie2 is not compatible with current GLIBC and glibc after I ran:

conda install -c asmeurer glibc

after this glibc was installed, conda return nothing, mamba return "segmentation fault" and

the bowtie2 was upgraded to 2.3.5.1. (the scenario is like this https://www.biostars.org/p/433973/). It is like I broke the conda and mamba. Do I need to uninstall "Ubuntu 20.04 on Windows"? or can I just delete whole miniconda3 folder and then re-install it?

thank you in advance

Chooseel

Upvotes: 1

Views: 1721

Answers (1)

merv
merv

Reputation: 76950

Broken Conda environments can be repaired externally using Micromamba (see this answer). No need to uninstall stuff. But if you want to start clean, it should be sufficient to reinstall Conda.

Please be aware that users generally will have a better experience not working from the base environment. Instead, create dedicated environments for the various tasks/projects. That is, use

mamba create -n bowtie -c conda-forge -c bioconda bowtie2

Also, mixing channels can lead to issues. Bioconda has very explicit requirements in channel priority:

channels:
  - conda-forge
  - bioconda
  - defaults

Upvotes: 2

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