A set of scripts and tools for the analysis of viral NGS data
|Versions||1.10.1, 1.11.0, 1.12.0, 1.12.1, 1.12.2, 1.13.2, 1.13.3, 1.13.4, 1.5.4, 1.5.5, 1.6.0, 1.6.1, 1.7.0, 1.7.1, 1.8.0, 1.9.0, 1.9.1, 1.9.2|
With an activated Bioconda channel (see 2. Set up channels), install with:
conda install viral-ngs
and update with:
conda update viral-ngs
This package makes use of GATK. Due to license restrictions, this recipe cannot distribute and install GATK directly as a dependency. To fully install GATK, you must download a licensed copy of GATK from the Broad Institute ( https://www.broadinstitute.org/gatk/download/ ), install this package (which will install the GATK wrapper package), and call “gatk-register /path/to/GenomeAnalysisTK[-$PKG_VERSION.tar.bz2|.jar]”, which will copy GATK into your conda environment. This package also makes use of Novoalign, which can be installed successfully as a conda package, however the unlicensed version of Novoalign runs in single-threaded mode. To enable multithreaded operation, it is necessary to supply a “novoalign.lic” license file and call “novoalign-license-register” to copy the license file into the conda environment.
A Docker container is available at https://quay.io/repository/biocontainers/viral-ngs.