gcnv environment problem

[ericblanc20]

Describe the bug
The gcnv tool in step sv_calling_wgs is currently broken because of difficulties in creating a working environment for it.

To Reproduce

1. Create a new conda environment from the gcnv environment description file
2. Try importing package gcnvkernel from the python console
3. The error is:

$ python
Python 3.10.13 | packaged by conda-forge | (main, Dec 23 2023, 15:36:39) [GCC 12.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import gcnvkernel
/data/cephfs-1/work/groups/cubi/users/blance_c/miniforge3/envs/test/lib/python3.10/site-packages/arviz/__init__.py:39: FutureWarning: 
ArviZ is undergoing a major refactor to improve flexibility and extensibility while maintaining a user-friendly interface.
Some upcoming changes may be backward incompatible.
For details and migration guidance, visit: https://python.arviz.org/en/latest/user_guide/migration_guide.html
  warn(
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/data/cephfs-1/work/groups/cubi/users/blance_c/miniforge3/envs/test/lib/python3.10/site-packages/gcnvkernel-0.9-py3.10.egg/gcnvkernel/__init__.py", line 1, in <module>
  File "/data/cephfs-1/work/groups/cubi/users/blance_c/miniforge3/envs/test/lib/python3.10/site-packages/pymc/__init__.py", line 49, in <module>
    from pymc import _version, gp, ode, sampling
  File "/data/cephfs-1/work/groups/cubi/users/blance_c/miniforge3/envs/test/lib/python3.10/site-packages/pymc/sampling/__init__.py", line 15, in <module>
    from pymc.sampling.forward import *
  File "/data/cephfs-1/work/groups/cubi/users/blance_c/miniforge3/envs/test/lib/python3.10/site-packages/pymc/sampling/forward.py", line 38, in <module>
    from fastprogress.fastprogress import progress_bar
  File "/data/cephfs-1/work/groups/cubi/users/blance_c/miniforge3/envs/test/lib/python3.10/site-packages/fastprogress/__init__.py", line 2, in <module>
    from .fastprogress import master_bar, progress_bar, force_console_behavior
  File "/data/cephfs-1/work/groups/cubi/users/blance_c/miniforge3/envs/test/lib/python3.10/site-packages/fastprogress/fastprogress.py", line 15, in <module>
    from fasthtml.common import *
  File "/data/cephfs-1/work/groups/cubi/users/blance_c/miniforge3/envs/test/lib/python3.10/site-packages/fasthtml/common.py", line 8, in <module>
    from apswutils import Database
  File "/data/cephfs-1/work/groups/cubi/users/blance_c/miniforge3/envs/test/lib/python3.10/site-packages/apswutils/__init__.py", line 2, in <module>
    from .db import *
  File "/data/cephfs-1/work/groups/cubi/users/blance_c/miniforge3/envs/test/lib/python3.10/site-packages/apswutils/db.py", line 21, in <module>
    apsw.bestpractice.connection_optimize,
AttributeError: module 'apsw.bestpractice' has no attribute 'connection_optimize'
>>> 

Note that this error is identical for gcnv wrapper environment with versions 4.6.1.0 & 4.6.2.0 of the gatk4 package. Only the ArviZ warning message is absent when using the 4.6.2.0 version.

Expected behavior
The package should be loaded without error.

Additional context
The following working environment has been kindly provided by @Nicolai-vKuegelgen.

To be used in snappy, it should replace the gcnv environment that was initially created in .snakemake/conda. For gatk4 version 4.6.1.0, the folder might be named 3ed885cdf7da468cd0c8671ff2d7706b_.

# This file may be used to create an environment using:
# $ conda create --name <env> --file <this file>
# platform: linux-64
# created-by: conda 24.11.3
@EXPLICIT
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