Bonjour, je souhaite lancer un pipeline Nextflow sur l'IFB, cependant il semblerait y avoir un conflit avec conda. En effet, le mauvais python est exécuté.
Quand on lance une session sur l'IFB voici le python exécuté /shared/ifbstor1/software/miniconda/bin/python et le $PATH ressemble à ça : /shared/ifbstor1/software/miniconda/bin:/shared/ifbstor1/software/miniconda/condabin:/opt/status_bars/status_bars:/shared/software/sinteractive:/shared/software/slurm-sinteractive:/shared/software/modules/4.6.1/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/go/1.14.4/bin:/opt/go/packages/bin:/shared/home/cvroland/.local/bin:/shared/home/cvroland/bin
Quand on active les modules pour nexflow (module load nextflow slurm-drmaa graphviz) le chemin vers python est /shared/ifbstor1/software/miniconda/envs/nextflow-23.04.1/bin/python et le $PATH est /shared/ifbstor1/software/miniconda/envs/graphviz-2.40.1/bin:/shared/ifbstor1/software/miniconda/envs/nextflow-23.04.1/bin:/shared/ifbstor1/software/miniconda/bin/:/shared/ifbstor1/software/miniconda/bin:/shared/ifbstor1/software/miniconda/condabin:/opt/status_bars/status_bars:/shared/software/sinteractive:/shared/software/slurm-sinteractive:/shared/software/modules/4.6.1/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/go/1.14.4/bin:/opt/go/packages/bin:/shared/home/cvroland/.local/bin:/shared/home/cvroland/bin
Maintenant, si j'active un environement conda (par exemple : conda activate pytorch-1.10.0), le python est resté sur /shared/ifbstor1/software/miniconda/envs/nextflow-23.04.1/bin/python. En effet, lorsque l'on regarde le $PATH /shared/ifbstor1/software/miniconda/envs/graphviz-2.40.1/bin:/shared/ifbstor1/software/miniconda/envs/nextflow-23.04.1/bin:/shared/ifbstor1/software/miniconda/envs/pytorch-1.10.0/bin:/shared/ifbstor1/software/miniconda/bin:/shared/ifbstor1/software/miniconda/condabin:/opt/status_bars/status_bars:/shared/software/sinteractive:/shared/software/slurm-sinteractive:/shared/software/modules/4.6.1/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/go/1.14.4/bin:/opt/go/packages/bin:/shared/home/cvroland/.local/bin:/shared/home/cvroland/bin, on voit que le chemin vers l'environnement conda (/shared/ifbstor1/software/miniconda/envs/pytorch-1.10.0/bin) est après le chemin vers le module nextflow. Ce dernier est donc prioritaire sur l'environnement conda.
Ce problème rend inutilisable conda dans un pipeline nextflow.