Conda

Mambaforge

A new module is available that includes mamba as the package manager - module load mambaforge/24.3.0

Conda Mirror

Currently we have a mirror for Conda to allow you to install packages without internet access. You should specify these local mirrors, when you want to create a new environment

conda create -c http://conda.repo.test.hhu.de/bioconda -c http://conda.repo.test.hhu.de/main -c http://conda.repo.test.hhu.de/conda-forge --override-channels --name my_environment

but also if you want  to install new packages

conda install -c http://conda.repo.test.hhu.de/bioconda -c http://conda.repo.test.hhu.de/main -c http://conda.repo.test.hhu.de/conda-forge --override-channels $PACKAGE_NAME

name: Example
channels:
  - nodefaults
  - http://conda.repo.test.hhu.de/bioconda
  - http://conda.repo.test.hhu.de/main
  - http://conda.repo.test.hhu.de/conda-forge

dependencies:
  - bwa = 0.7.17
  - samtools = 1.10
  - bcftools = 1.10.2

.condarc

To make your life super easy and just ignore all of the above (and thus also keep your existing .yaml files) you can also just create a .condarc file in your home directory with the following contents (this handles the redirection of the channels to the custom hhu ones for you):

channel_alias: http://conda.repo.test.hhu.de/
channel_priority: strict
channels:
  - conda-forge
  - main
  - bioconda

You can also directly copy this file from our /software/conda directory:

cp /software/conda/condarc.hhu /home/$USER/.condarc

There are currently five different conda modules.

For normal usage utilize Miniconda/3. If you want to use conda within snakemake or have other specific needs you can try Miniconda/3_noInit or Miniconda/3_snakemake.

Miniconda/3.1 uses a newer version of Python (3.10.8) and pip.

mambaforge/24.3.0 includes mamba as the packet manager, this is often much faster than conda.

                                       Usage : mamba create -n yourimage; conda activate yourimage; mamba install newpackage

If activating your conda environment works for you in interactive mode but not in batch mode, then you might need to source your files .bashrc and .bash_profile. This is because in interactive mode you'll get a login shell but in batch mode not. In your jobscript such a solution could look as follows:

#!/bin/bash
#PBS -l select=1:ncpus=X:mem=XGB
#PBS -l walltime=X:00:00
#PBS -A 'XXX'

# source bash
source $HOME/.bashrc
source $HOME/.bash_profile
conda activate SOME_ENV