errors during env creation and run local conda test

[MSajek]

Hi,
I want to use PAQR2 and find the following issues:
During the env creation I had the following error:

Pip subprocess error:
ERROR: Package 'requests' requires a different Python: 3.7.4 not in '>=3.8'

failed

CondaEnvException: Pip failed

To solve this I installed requests compatible with python3.7.4 (2.26.0) with pip and then snakemake 6.5.5.

Next, when run

bash execute/run_local_conda_test.sh

I needed to downgrade pulp to 2.6.0 and tabulate to 0.8.9 to be able to succesfuly run the tests.
Thus you may consider to update environment.yml:

###############################################################################
#
#   Packages in conda virtual environment for PAQR
#
#   AUTHOR: Maciej_Bak
#   AFFILIATION: University_of_Basel
#   AFFILIATION: Swiss_Institute_of_Bioinformatics
#   CONTACT: maciej.bak@unibas.ch
#   CREATED: 20-03-2020
#   LICENSE: Apache_2.0
#
###############################################################################
---

name: paqr2

channels:
  - conda-forge
  - defaults

dependencies:
  - bash=4.4.18
  - python=3.7.4
  - pip=20.0.2
  - pandas=1.0.1
  - graphviz=2.40.1
  - mamba
  - pip:
    - requests==2.26.0
    - pulp==2.6.0
    - tabulate==0.8.9
    - snakemake==6.5.5

...

Best,
Marcin

[AngryMaciek]

Thanks, good point. However, its been years since I left the Zavolan Lab and I am not maintaining their code anymore, this should be assigned to appropriate maintainer.