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I'm installing IsoQuant as part of a module system on a large HPC cluster, and I use virtualenv (not conda) to isolate python dependencies. pyfaidx uses from packaging.version import Version to check the Biopython version, and while this is part of a standard python installation (and would be within a conda environment populated with a python) it is not installed within a virtualenv populated by pip3 install -r requirements.txt. This results in an error cascade that ends with
ImportError: BioPython >= 1.73 must be installed to read block gzip files.
because pyfaidx cannot check the Biopython version installed within the virtualenv.
Ideally should be marked as a dependency by pyfaidx, but adding it to IsoQuant's requirement.txt here solves the problem as well.
The text was updated successfully, but these errors were encountered:
I'm installing IsoQuant as part of a module system on a large HPC cluster, and I use virtualenv (not conda) to isolate python dependencies. pyfaidx uses
from packaging.version import Version
to check the Biopython version, and while this is part of a standard python installation (and would be within a conda environment populated with a python) it is not installed within a virtualenv populated bypip3 install -r requirements.txt
. This results in an error cascade that ends withbecause pyfaidx cannot check the Biopython version installed within the virtualenv.
Ideally should be marked as a dependency by pyfaidx, but adding it to IsoQuant's
requirement.txt
here solves the problem as well.The text was updated successfully, but these errors were encountered: