add deprecated.hook to mark tools no installable anymore
Ajout du fichier "deprecated.hook" sur les outils suivants:
- alientrimmer/0.4.1
Le paquet n'existe plus en 0.4.1: https://anaconda.org/aghozlane/alientrimmer/files
ResolvePackageNotFound: aghozlane::alientrimmer=0.4.1.
- busco/4.0.5 (installé en utilisant mamba)
$ busco --version
Bio.Alphabet has been removed from Biopython. In many cases, the alphabet can simply be ignored and removed from scripts. In a few cases, you may need to specify the ``molecule_type`` as an annotation on a SeqRecord for your script to work correctly. Please see https://biopython.org/wiki/Alphabet for more information.
There was a problem installing BUSCO or importing one of its dependencies. See the user guide and the GitLab issue board (https://gitlab.com/ezlab/busco/issues) if you need further assistance.
- pyscenic/0.10.0
pyscenic -h
/gpfs/softs/contrib/ifb/miniconda3/envs/pyscenic-0.10.0/lib/python3.6/site-packages/dask/config.py:161: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.
data = yaml.load(f.read()) or {}
/gpfs/softs/contrib/ifb/miniconda3/envs/pyscenic-0.10.0/lib/python3.6/site-packages/dask/dataframe/utils.py:13: FutureWarning: pandas.util.testing is deprecated. Use the functions in the public API at pandas.testing instead.
import pandas.util.testing as tm
Traceback (most recent call last):
File "/gpfs/softs/contrib/ifb/miniconda3/envs/pyscenic-0.10.0/bin/pyscenic", line 5, in <module>
from pyscenic.cli.pyscenic import main
File "/gpfs/softs/contrib/ifb/miniconda3/envs/pyscenic-0.10.0/lib/python3.6/site-packages/pyscenic/cli/pyscenic.py", line 20, in <module>
from pyscenic.rnkdb import opendb, RankingDatabase
File "/gpfs/softs/contrib/ifb/miniconda3/envs/pyscenic-0.10.0/lib/python3.6/site-packages/pyscenic/rnkdb.py", line 12, in <module>
from pyarrow.feather import write_feather, FeatherReader
ImportError: cannot import name 'FeatherReader'
Edited by David Benaben