Anaconda

Anaconda is a free and open-source distribution of the Python.

For better performances Anaconda python V3 et V2 are installed with Several optimized scientific packages.

In console, check the available modules:

$ module avail lang/python/anaconda
lang/python/anaconda/2.7 lang/python/anaconda/3.7 lang/python/anaconda/3.8

load python version, for example:

$ module load lang/python/anaconda/3.8

Check for installed packages:

$ conda list

You may need to install additional package without having root access. We instead recommend building a virtual environment locally and install packages there. But before we need to tell conda to use WORK to store pkgs. Run commands below only once :

$ conda config --add pkgs_dirs $WORK/.conda/pkgs
$ conda config --add envs_dirs $WORK/.conda/envs

1. Create a conda environment

   $ conda create -y --prefix $WORK/conda-env python=3.7.4 

   replace conda-env by a valid name.

2. Activate the environment you just created

   $ conda activate $WORK/conda-env  

3. Download and install the conda package in the environment

    $ conda install package

   replace package by the package you wan to install, for example panda

4. Run your analysis from within the environment
5. Deactivating environment, once you are done with your analysis- you can deactivate the conda environment by running the command

   $ conda deactivate

Here is a simple SGE script that load anaconda 3.7, activate conda env called conda-env and then run a python program.

anaconda.sge

#!/bin/bash
 
#$ -q all.q
 
#$ -l h_vmem=6G ## job will cancel if memory exceed
 
#$ -N Test_anaconda
 
module load lang/python/anaconda/3.7
 
## load conda, activate env called conda-env and run conda program
 
conda activate $WORK/conda-env && python conda_Program.py