Bonjour,
Serait-il possible d'installer Nanopack sur le cluster ?
Merci d'avance !
Bonjour Denis,
Nous pouvons installer nanoplot, nanoqc et nanofilt qui ont été packagé avec conda.
Mais vous pouvez aussi simplement installer NanoPack dans votre environnement:
# Utiliser une version de python
module load python/3.9
# Lancer l'installation
pip install nanopack
Les outils/script (NanoComp, NanoFilt, NanoLyse, NanoPlot et NanoStat) sont alors disponibles:
$ NanoFilt --version
NanoFilt 2.8.0
A noter, que pip va installer NanoPack dans votre /home (équivalent de l'option --user de pip) puisqu'il ne peut écrire dans le répertoire principal.
Que préférez-vous ?
J'ai pu installer Nanopack sur mon /home comme indiqué.
Merci.
Bonjour,
Je reviens vers vous car Nanopack que j'ai installé sur mon /home il y a un an comme indiqué ci-dessus, ne fonctionne plus depuis quelques jours.
Je n'en comprends pas la raison.
[dfilloux@clust-slurm-client work]$ module list
No Modulefiles Currently Loaded.
[dfilloux@clust-slurm-client work]$ NanoFilt --version
-bash: /shared/home/dfilloux/.local/bin/NanoFilt: /shared/ifbstor1/software/miniconda/envs/python-3.9/bin/python3.9: bad interpreter: No such file or directory
[dfilloux@clust-slurm-client work]$ module load python/3.9
[dfilloux@clust-slurm-client work]$ NanoFilt --version
-bash: /shared/home/dfilloux/.local/bin/NanoFilt: /shared/ifbstor1/software/miniconda/envs/python-3.9/bin/python3.9: bad interpreter: No such file or directory
Bonjour Denis,
Il y a quelques semaines, les environnements Python 3.7 et 3.9 ont été revus en profondeur (afin d'y inclure les librairies de chargement de données, visualisation et "machine learning" les plus courantes).
Et je crains qu'il y ait un effet de bord avec votre installation.
Le plus simple est je pense de réinstaller:
module load python/3.9
pip install nanopack
Pouvez-vous essayer ?
Oui, j'ai eu la même idée mais même résultat...
Voici le rapport de la réinstallation :
[dfilloux@clust-slurm-client work]$ module load python/3.9
[dfilloux@clust-slurm-client work]$ pip install nanopack
Defaulting to user installation because normal site-packages is not writeable
Requirement already satisfied: nanopack in /shared/ifbstor1/home/dfilloux/.local/lib/python3.9/site-packages (1.1.0)
Requirement already satisfied: NanoFilt>=2.7.1 in /shared/ifbstor1/home/dfilloux/.local/lib/python3.9/site-packages (from nanopack) (2.8.0)
Requirement already satisfied: NanoPlot>=1.30.0 in /shared/ifbstor1/home/dfilloux/.local/lib/python3.9/site-packages (from nanopack) (1.39.0)
Requirement already satisfied: NanoComp>=1.11.2 in /shared/ifbstor1/home/dfilloux/.local/lib/python3.9/site-packages (from nanopack) (1.17.0)
Requirement already satisfied: nanoget>=1.13.2 in /shared/ifbstor1/home/dfilloux/.local/lib/python3.9/site-packages (from nanopack) (1.16.1)
Requirement already satisfied: NanoLyse>=1.1.3 in /shared/ifbstor1/home/dfilloux/.local/lib/python3.9/site-packages (from nanopack) (1.2.0)
Requirement already satisfied: nanomath>=0.23.3 in /shared/ifbstor1/home/dfilloux/.local/lib/python3.9/site-packages (from nanopack) (1.2.1)
Requirement already satisfied: NanoStat>=1.2.1 in /shared/ifbstor1/home/dfilloux/.local/lib/python3.9/site-packages (from nanopack) (1.6.0)
Requirement already satisfied: nanoQC>=0.9.3 in /shared/ifbstor1/home/dfilloux/.local/lib/python3.9/site-packages (from nanopack) (0.9.4)
Requirement already satisfied: pandas in /shared/ifbstor1/software/miniconda/envs/python-pytorch-tensorflow-3.9-1.11.0-2.6.2/lib/python3.9/site-packages (from NanoComp>=1.11.2->nanopack) (1.4.2)
Requirement already satisfied: plotly>=3.4.2 in /shared/ifbstor1/software/miniconda/envs/python-pytorch-tensorflow-3.9-1.11.0-2.6.2/lib/python3.9/site-packages (from NanoComp>=1.11.2->nanopack) (5.8.2)
Requirement already satisfied: psutil in /shared/ifbstor1/home/dfilloux/.local/lib/python3.9/site-packages (from NanoComp>=1.11.2->nanopack) (5.9.0)
Requirement already satisfied: numpy>=1.16.5 in /shared/ifbstor1/software/miniconda/envs/python-pytorch-tensorflow-3.9-1.11.0-2.6.2/lib/python3.9/site-packages (from NanoComp>=1.11.2->nanopack) (1.19.5)
Requirement already satisfied: pyarrow in /shared/ifbstor1/home/dfilloux/.local/lib/python3.9/site-packages (from NanoComp>=1.11.2->nanopack) (6.0.1)
Requirement already satisfied: biopython in /shared/ifbstor1/software/miniconda/envs/python-pytorch-tensorflow-3.9-1.11.0-2.6.2/lib/python3.9/site-packages (from NanoFilt>=2.7.1->nanopack) (1.79)
Requirement already satisfied: pysam>0.10.0.0 in /shared/ifbstor1/home/dfilloux/.local/lib/python3.9/site-packages (from nanoget>=1.13.2->nanopack) (0.18.0)
Requirement already satisfied: mappy>=2.2 in /shared/ifbstor1/home/dfilloux/.local/lib/python3.9/site-packages (from NanoLyse>=1.1.3->nanopack) (2.24)
Requirement already satisfied: Python-Deprecated in /shared/ifbstor1/home/dfilloux/.local/lib/python3.9/site-packages (from nanomath>=0.23.3->nanopack) (1.1.0)
Requirement already satisfied: kaleido in /shared/ifbstor1/home/dfilloux/.local/lib/python3.9/site-packages (from NanoPlot>=1.30.0->nanopack) (0.2.1)
Requirement already satisfied: python-dateutil in /shared/ifbstor1/software/miniconda/envs/python-pytorch-tensorflow-3.9-1.11.0-2.6.2/lib/python3.9/site-packages (from NanoPlot>=1.30.0->nanopack) (2.8.2)
Requirement already satisfied: scipy in /shared/ifbstor1/software/miniconda/envs/python-pytorch-tensorflow-3.9-1.11.0-2.6.2/lib/python3.9/site-packages (from NanoPlot>=1.30.0->nanopack) (1.8.1)
Requirement already satisfied: bokeh in /shared/ifbstor1/software/miniconda/envs/python-pytorch-tensorflow-3.9-1.11.0-2.6.2/lib/python3.9/site-packages (from nanoQC>=0.9.3->nanopack) (2.3.3)
Requirement already satisfied: pytz>=2020.1 in /shared/ifbstor1/software/miniconda/envs/python-pytorch-tensorflow-3.9-1.11.0-2.6.2/lib/python3.9/site-packages (from pandas->NanoComp>=1.11.2->nanopack) (2022.1)
Requirement already satisfied: tenacity>=6.2.0 in /shared/ifbstor1/software/miniconda/envs/python-pytorch-tensorflow-3.9-1.11.0-2.6.2/lib/python3.9/site-packages (from plotly>=3.4.2->NanoComp>=1.11.2->nanopack) (8.0.1)
Requirement already satisfied: six>=1.5 in /shared/ifbstor1/software/miniconda/envs/python-pytorch-tensorflow-3.9-1.11.0-2.6.2/lib/python3.9/site-packages (from python-dateutil->NanoPlot>=1.30.0->nanopack) (1.15.0)
Requirement already satisfied: typing-extensions>=3.7.4 in /shared/ifbstor1/software/miniconda/envs/python-pytorch-tensorflow-3.9-1.11.0-2.6.2/lib/python3.9/site-packages (from bokeh->nanoQC>=0.9.3->nanopack) (3.7.4.3)
Requirement already satisfied: tornado>=5.1 in /shared/ifbstor1/software/miniconda/envs/python-pytorch-tensorflow-3.9-1.11.0-2.6.2/lib/python3.9/site-packages (from bokeh->nanoQC>=0.9.3->nanopack) (6.1)
Requirement already satisfied: Jinja2>=2.9 in /shared/ifbstor1/software/miniconda/envs/python-pytorch-tensorflow-3.9-1.11.0-2.6.2/lib/python3.9/site-packages (from bokeh->nanoQC>=0.9.3->nanopack) (3.1.2)
Requirement already satisfied: PyYAML>=3.10 in /shared/ifbstor1/software/miniconda/envs/python-pytorch-tensorflow-3.9-1.11.0-2.6.2/lib/python3.9/site-packages (from bokeh->nanoQC>=0.9.3->nanopack) (6.0)
Requirement already satisfied: pillow>=7.1.0 in /shared/ifbstor1/software/miniconda/envs/python-pytorch-tensorflow-3.9-1.11.0-2.6.2/lib/python3.9/site-packages (from bokeh->nanoQC>=0.9.3->nanopack) (9.1.1)
Requirement already satisfied: packaging>=16.8 in /shared/ifbstor1/software/miniconda/envs/python-pytorch-tensorflow-3.9-1.11.0-2.6.2/lib/python3.9/site-packages (from bokeh->nanoQC>=0.9.3->nanopack) (21.3)
Requirement already satisfied: MarkupSafe>=2.0 in /shared/ifbstor1/software/miniconda/envs/python-pytorch-tensorflow-3.9-1.11.0-2.6.2/lib/python3.9/site-packages (from Jinja2>=2.9->bokeh->nanoQC>=0.9.3->nanopack) (2.1.1)
Requirement already satisfied: pyparsing!=3.0.5,>=2.0.2 in /shared/ifbstor1/software/miniconda/envs/python-pytorch-tensorflow-3.9-1.11.0-2.6.2/lib/python3.9/site-packages (from packaging>=16.8->bokeh->nanoQC>=0.9.3->nanopack) (3.0.9)
Il faut au préalable désinstaller la version.
pip uninstall nanopack
# Ou plus directement renomer/supprimer le dossier local:
mv /shared/ifbstor1/home/dfilloux/.local/lib/python3.9 /shared/ifbstor1/home/dfilloux/.local/lib/python3.9-backup-2022-07-07
C'est bon.
Cela fonctionne maintenant.
"pip uninstall nanopack" n'a pas suffit.
Seul le mv a permis de réinstaller nanopack.
Merci.
Cordialement.
Ok, c'est noté.
Bonne continuation