BEAR Applications

OptiType 1.3.2-foss-2018b-Python-2.7.15

Deprecated: Use of this version of OptiType is deprecated. More information on our Applications Support and Retention Policy.

There is a newer version of OptiType

OptiType is a novel HLA genotyping algorithm based on integer linear programming, capable of producing accurate 4-digit HLA genotyping predictions from NGS data by simultaneously selecting all major and minor HLA Class I alleles.

Accessing OptiType 1.3.2-foss-2018b-Python-2.7.15

To load the module for OptiType 1.3.2-foss-2018b-Python-2.7.15 please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):

module load OptiType/1.3.2-foss-2018b-Python-2.7.15

BEAR Apps Version

2018b

Architectures

EL8-cascadelake — EL8-haswell — Ubuntu20.04-haswell

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.

More Information

For more information visit the OptiType website.

Dependencies

This version of OptiType has a direct dependency on: foss/2018b future/0.16.0-foss-2018b-Python-2.7.15 GLPK/4.65-GCCcore-7.3.0 HDF5/1.10.2-foss-2018b matplotlib/2.2.3-foss-2018b-Python-2.7.15 Pyomo/5.5.0-foss-2018b-Python-2.7.15 Pysam/0.15.1-foss-2018b-Python-2.7.15 PyTables/3.4.4-foss-2018b-Python-2.7.15 Python/2.7.15-foss-2018b SAMtools/1.9-foss-2018b SeqAn/2.4.0-foss-2018b

Other Versions

These versions of OptiType 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 7th June 2019