pcgr 1.0.3
There is a newer version of pcgr
The Personal Cancer Genome Reporter (PCGR) is a stand-alone software package for functional annotation and translation of individual tumor genomes for precision cancer medicine.Accessing pcgr 1.0.3
To load the module for pcgr 1.0.3 please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):
module load bear-apps/2021b
module load pcgr/1.0.3
BEAR Apps Version
Architectures
EL8-cascadelake — EL8-haswell — EL8-icelake
The listed architectures consist of two part: OS-CPU.
- BlueBEAR: The OS used on BlueBEAR is represented by EL and there are several different processor (CPU) types available on BlueBEAR. More information about the processor types on BlueBEAR is available on the BlueBEAR Job Submission page.
- BEAR and CaStLeS Cloud VMs: These VMs can have one of two OSes. Those with access to a BEAR Cloud or CaStLeS VM should check that the listed architectures for an application include the OS of VM being used. The VMs, irrespective of OS, will use the haswell CPU type.
pcgr Databases
The pcgr databases, are available in ${BASK_APPS_DATA}/pcgr
. Inside that folder you will find folder(s) dated by download date. Each dated folder contains all of the databases that can be downloaded from http://insilico.hpc.uio.no/pcgr/pcgr.databundle.${GENOME}.${BUNDLE_VERSION}.tgz
where GENOME
is either "grch38" or "grch37" and BUNDLE_VERSION is the date of the genome version.
Running pcgr
Running pcgr you have to ensure your options point to the correct location you can do pcgr -h
to see all the available options. Key options that must be stated are pcgr_dir $BB_APPS_DIR/pcgr/20220203
the location of the data and genome_assembly $GENOME
one of the two available data bundles.
More Information
For more information visit the pcgr website.
Dependencies
This version of pcgr has a direct dependency on: pcgrr/1.0.3
Other Versions
These versions of pcgr are available on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs). These will be retained in accordance with our Applications Support and Retention Policy.
Last modified on 11th November 2022