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 0.15.2-foss-2019a
To load the module for Pysam 0.15.2-foss-2019a please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):
module load Pysam/0.15.2-foss-2019a
There is a GPU enabled version of this module: Pysam 0.15.2-fosscuda-2019a
BEAR Apps Version
For more information visit the Pysam website.
This version of Pysam has a direct dependency on: cURL/7.63.0-GCCcore-8.2.0 foss/2019a ncurses/6.1-GCCcore-8.2.0 Python/2.7.15-GCCcore-8.2.0 Python/3.7.2-GCCcore-8.2.0 XZ/5.2.4-GCCcore-8.2.0
This version of Pysam is compatible with multiple vesions of Python. At any time, only one of the versions of Python can be active and the desired version of Python should be loaded before loading this version of Pysam.
This version of Pysam is a direct dependent of: ALFA/1.1.1-foss-2019a-Python-3.7.2 MMSplice/1.0.3-foss-2019a-Python-3.7.2 pybedtools/0.8.0-foss-2019a rMATS/4.0.2-foss-2019a-Python-2.7.15 SpliceAI/1.3-foss-2019a-Python-3.7.2 velocyto/0.17.17-foss-2019a-Python-3.7.2 WhatsHap/0.18-foss-2019a-Python-3.7.2
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 22nd July 2019