libgsl.so.25 potential issue

AdamSorrel commented 2 years ago

Hi, I am not certain to which extent this is an issue, but I thought you might want to check it. Granted, I have my fastANI installed as a part of the GTDBTK package through anaconda so I reckon this could be their problem. In a nutshell the recipe in Anaconda required the gsl package to be >2.7, however the current generic version is 2.7.1 which provides only libgsl.so.27, which results in the following error:

fastANI: error while loading shared libraries: libgsl.so.25: cannot open shared object file: No such file or directory

Currently the workaround seems to be to downgrade to a gsl version 2.7, for example:

 mamba install -c conda-forge gsl=2.7=he838d99_0

Unfortunately I had to force a specific build, because just plain downgrading to 2.7 doesn't seem to cut it. I don't know if this might be some older version of fastANI in GTDBTK, in which case I would be happy to let them know to at least post this as a requirement in their installation.

Thanks a lot for the great program!

cjain7 commented 2 years ago

I request you to inform GTDBTK authors as well. They may have a better solution in mind.

cjain7 commented 2 years ago

FYI https://www.ramanean.com/solved-libgsl-so-25-cannot-open-shared-object-file-no-such-fle-or-directory/

rhysnewell commented 2 years ago

Hi folks,

Looks like this might be an issue with the conda package for FastANI v1.33. Downgrading to v1.32 works fine but it requires the conda environment to be recreated due to package conflicts: https://github.com/Ecogenomics/GTDBTk/issues/370

Cheers, Rhys

cjain7 commented 2 years ago

cc'ing @rpetit3 and @jlumpe

cjain7 commented 2 years ago

We had recently updated conda recipe of FastANI #95

rpetit3 commented 2 years ago

Try downgrading gsl to 2.6

samnooij commented 2 years ago

I ran into the same issue with FastANI version 1.33, installed via conda. Downgrading gsl did not work, but gave the error:

Encountered problems while solving:
  - package fastani-1.33-h0fdf51a_1 requires gsl >=2.7,<2.8.0a0, but none of the providers can be installed

What seemed to have worked is create a symbolic link from libgsl.so.27, which I did have, to libgsl.so.25. (In the directory /path/to/miniconda3/envs/fastani/lib/.) This can hardly be called a solution, but it is a workaround that seems to work for me now.

To install FastANI, I used the following YAML file:

name: fastani

channels:
- defaults
- bioconda
- conda-forge

dependencies:
- fastani=1.33

and the command mamba env create -f fastani.yaml

ParBLiSS / FastANI

libgsl.so.25 potential issue #96