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Install Miniconda

Small tutorial on how install and run miniconda on HPC cluster

  1. Login into you login machine
  2. Download Miniconda into you local home
wget https://repo.anaconda.com/miniconda/Miniconda2-latest-Linux-x86_64.sh
  1. Execute Miniconda
chmod +x Miniconda2-latest-Linux-x86_64.sh (give execution permission fo file)

./Miniconda2-latest-Linux-x86_64.sh

Welcome to Miniconda2 4.6.14

In order to continue the installation process, please review the license
agreement.
Please, press ENTER to continue

.... 

Do you wish the installer to initialize Miniconda2
by running conda init? [yes|no]
[no] >>> no 

...
  1. Run miniconda
miniconda2/bin/conda
  1. Load conda environment
source /home/csys/jpina/miniconda2/etc/profile.d/conda.sh
  1. Load conda environment in your submission script
cat test_submit.sh 

#!/bin/bash
# Load user environment during job excution 
#$ -V   

# Start jobs at the submisssion path 
#$ -cwd 

# Call parallell environment "mp", and excute in 4 cores 
#$ -pe mp 4

# Queue selection 
#$ -q hpc

# Load miniconda 
source  /home/csys/jpina/miniconda2/etc/profile.d/conda.sh

NOTE_ Loading conda environment can lead to conflit with 'modules load' commands so it's not recommended users to load both environments

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