Lefse Installation Issue

[Hoeferlin]

Hello,

I have been trying for the last two days to install lefse on a cluster at my university. I have verified that all R libraries have been installed along with conda / python / etc. However, every time I try to install lefse, there are conflicts at the 'solving environment' phase. I have tried different versions of python following similar troubleshooting posts to no avail. Does anyone have a suggestion? Thank you!

(base) [gfh16@compt341 ~]$ conda create -n thelefse python=3.7
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(base) [gfh16@compt341 ~]$ conda activate thelefse
(thelefse) [gfh16@compt341 ~]$ conda install -c bioconda lefse
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: |
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

Package libgcc-ng conflicts for:
sqlite -> libgcc-ng[version='>=10.3.0|>=12|>=9.4.0|>=9.3.0|>=7.5.0|>=7.3.0|>=4.9|>=11.2.0|>=7.2.0']
libzlib -> libgcc-ng[version='>=10.3.0|>=12|>=7.5.0']
setuptools -> python[version='>=3.7'] -> libgcc-ng[version='>=10.3.0|>=12|>=9.4.0|>=9.3.0|>=7.5.0|>=7.3.0|>=4.9|>=11.2.0|>=7.2.0']
xz -> libgcc-ng[version='>=11.2.0|>=12|>=7.5.0|>=7.3.0|>=4.9|>=7.2.0']
libgcc-ng
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.
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Package wheel conflicts for:
python=3.7 -> pip -> wheel
wheel
pip -> wheelThe following specifications were found to be incompatible with your system:

  - feature:/linux-64::__glibc==2.28=0
  - feature:|@/linux-64::__glibc==2.28=0
  - libffi -> libgcc-ng[version='>=9.4.0'] -> __glibc[version='>=2.17']
  - libgcc-ng -> __glibc[version='>=2.17']
  - libnsl -> libgcc-ng[version='>=9.4.0'] -> __glibc[version='>=2.17']
  - libstdcxx-ng -> __glibc[version='>=2.17']
  - libzlib -> libgcc-ng[version='>=10.3.0'] -> __glibc[version='>=2.17']
  - ncurses -> libgcc-ng[version='>=10.3.0'] -> __glibc[version='>=2.17']
  - python=3.7 -> libgcc-ng[version='>=9.4.0'] -> __glibc[version='>=2.17']
  - readline -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
  - sqlite -> libgcc-ng[version='>=10.3.0'] -> __glibc[version='>=2.17']
  - tk -> libgcc-ng[version='>=9.4.0'] -> __glibc[version='>=2.17']
  - xz -> libgcc-ng[version='>=7.5.0'] -> __glibc[version='>=2.17']

Your installed version is: 2.28

Note that strict channel priority may have removed packages required for satisfiability.

[caonetto]

I am having the same issue, Im unable to install lefse succesfully through conda, ive tried multiple combinations and there are always incompatibilities. The Galaxy server is down as well so it seems to be imposible to run lefse at this stage. Any recommendations?

[qingzengLi]

I am having the same issue, Im unable to install lefse succesfully through conda, ive tried multiple combinations and there are always incompatibilities. The Galaxy server is down as well so it seems to be imposible to run lefse at this stage. Any recommendations?

I successfully installed lefse using pip

[sdgamboa]

I solved incompatibilities with conda config --set channel_priority flexible

[MonicaSteffi]

I solved incompatibilities with conda config --set channel_priority flexible

I tried with this too, But couldn't manage it. Is there any other to solve this?

[sdgamboa]

@MonicaSteffi this worked for me (Pop OS):

conda create -n lefse
conda activate lefse
## conda config --set channel_priority flexible # This might be necessary
conda install -c bioconda lefse