Currently we have a mirror for Conda to allow you to install packages without internet access | Codeblock |
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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 |
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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 |
To activate conda environments in batch-script mode please source your .bashrc and .bash_profile in submission script before you activate the conda environment | Codeblock |
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#!/bin/bash
#PBS -l select=1:ncpus=X:mem=XGB
#PBS -l walltime=X:00:00
#PBS -A 'XXX'
# source bash
source /home/USER/.bashrc
source /home/USER/.bash_profile
conda activate SOME_ENV |
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