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marbl / MashMap

A fast approximate aligner for long DNA sequences
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libblis.so.4 not found via bioconda installation #72

Open mxwang66 opened 3 days ago

mxwang66 commented 3 days ago

Happened on gho and p00 Conda install command:

conda create -n mashmap mashmap --channel conda-forge --channel bioconda --strict-channel-priority

Error message:

(mashmap) xw66@p00:~/nextflow$ mashmap -h
mashmap: error while loading shared libraries: libblis.so.4: cannot open shared object file: No such file or directory

A temporary solution:

  1. Compile from source on gho, following INSTALL.txt (no need to install other dependencies).
  2. Add the compiled binary to PATH.
  3. Run mashmap on gho. If run on p00, the error below will be raised: 
    xw66@p00:~/nextflow$ mashmap -h
mashmap: error while loading shared libraries: libgsl.so.25: cannot open shared object file: No such file or directory
skoren commented 2 days ago

I encountered this error in the verkko recipe as well. This is an issue caused by bioconda maintenance updates which released a new build version 1 month ago breaking the artifacts: https://github.com/bioconda/bioconda-recipes/issues/52321. Not sure if there is a way to request build0 for the same version or you could just request an older MashMap as a workaround.

mxwang66 commented 2 days ago

Thanks @skoren ! I tried to install build0 and it worked @bkille 

conda create -n mashmap mashmap=3.1.3=h07ea13f_0 --channel conda-forge --channel bioconda --strict-channel-priority

The build string can be found at https://anaconda.org/bioconda/mashmap/files

So it seems the dependency should be linked to libblas but now it's linked to libblis? I noticed libgsl is not found either (in your bioconda issue), which was the error I got when I compiled from source from one of our servers.

bkille commented 2 days ago

@mxwang66 @skoren Thanks for bringing this to my attention. I opened a PR here to try and fix the current v3.1.3 build. Will keep you posted.