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Info
titleLatest Information

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


Codeblock
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

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


Codeblock
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):

Codeblock
channel_alias: http://conda.repo.test.hhu.de/

default_channels:
  - http://conda.repo.test.hhu.de/main
  - http://conda.repo.test.hhu.de/bioconda
  - http://conda.repo.test.hhu.de/conda-forge



Info
titlemodules

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.


Info
titleHinweis

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:

Codeblock
#!/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