pcgr 1.2.0

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 1.2.0

To load the module for pcgr 1.2.0 please use this command on the BEAR systems (BlueBEAR, BEAR Cloud VMs, and CaStLeS VMs):

module load bear-apps/2022a
module load pcgr/1.2.0

BEAR Apps Version

2022a

Architectures

EL8-cascadelakeEL8-haswellEL8-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 Cloud and CaStLeS 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/1.2.0

Other Versions

These versions of pcgr are available on the BEAR systems (BlueBEAR, BEAR Cloud VMs, and CaStLeS VMs). These will be retained in accordance with our Applications Support and Retention Policy.

Version BEAR Apps Version
1.0.3 2021b

Last modified on 16th February 2023