Deprecated: Use of this version of Pysam is deprecated. More information on our Applications Support and Retention Policy.
There is a newer version of PysamPysam is a python module for reading and manipulating Samfiles. It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.
Accessing Pysam 0.15.1-foss-2018b-Python-3.6.6
To load the module for Pysam 0.15.1-foss-2018b-Python-3.6.6 please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):
module load Pysam/0.15.1-foss-2018b-Python-3.6.6
BEAR Apps Version
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.
For more information visit the Pysam website.
This version of Pysam has a direct dependency on: cURL/7.60.0-GCCcore-7.3.0 foss/2018b ncurses/6.1-GCCcore-7.3.0 Python/3.6.6-foss-2018b
This version of Pysam is a direct dependent of: amplimap/0.4.5-foss-2018b-Python-3.6.6 ariba/2.13.5-foss-2018b-Python-3.6.6 OptiType/1.3.2-foss-2018b-Python-3.6.6 WhatsHap/0.18-foss-2018b-Python-3.6.6
These versions of Pysam 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 3rd June 2019