Versionen im Vergleich

Alte Version 5

changes.mady.by.user Houwaart, Torsten

Gespeichert am

verglichen mit

Neue Version 6

changes.mady.by.user Houwaart, Torsten

Gespeichert am

Schlüssel

  • Diese Zeile wurde hinzugefügt.
  • Diese Zeile wurde entfernt.
  • Formatierung wurde geändert.

...

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/main -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



Info
titlemodules

There are currently four 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`.


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


...