Setting up the environment
Introduction
Some preparations are required before downloading the GENIE data and creating
additional auxiliary files needed by the genie
package. Please follow the
instructions below to set up your environment.
Install mamba
If you haven't done so already anyway, please install mamba
, the next
generation replacement for conda
. One of the advantages of mamba
is that
it is much faster than conda
.
Please see the Mamba Installation Instructions on how to install mamba
.
Create a virtual environment for genie
Install genie package
Install genie package
Install packages and programs
Install Illumina Annotator and icaparser module
For the normalization and annotation of mutations from GENIE, a working setup of
Illumina Connected Annotations (previously known as Nirvana) and the
icaparser
module is needed. Setting
up this environment is beyond the scope of this document, please see the
documentation of icaparser
for
instructions.