BEAR Applications: Pysam 0.15.3-GCC-8.3.0 (for BlueBEAR, BEARCloud VMs, and CaStLeS VMs)

Pysam 0.15.3-GCC-8.3.0

Pysam 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 0.15.3-GCC-8.3.0

To load the module for Pysam 0.15.3-GCC-8.3.0 please use this command on the BEAR systems (BlueBEAR, BEAR Cloud VMs, and CaStLeS VMs):

module load Pysam/0.15.3-GCC-8.3.0

BEAR Apps Version

2020h

More Information

For more information visit the Pysam website.

Dependencies

This version of Pysam has a direct dependency on: cURL/7.66.0-GCCcore-8.3.0 GCC/8.3.0 ncurses/6.1-GCCcore-8.3.0 Python/2.7.16-GCCcore-8.3.0 Python/3.7.4-GCCcore-8.3.0 XZ/5.2.4-GCCcore-8.3.0

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.

Required By

This version of Pysam is a direct dependent of: cgat/0.6.5-foss-2019b-Python-3.7.4 HTSeq/0.12.4-foss-2019b-Python-3.7.4 HTSeq/0.12.4-foss-2019b-Python-2.7.16 LongQC/1.0-foss-2019b-Python-3.7.4 pybedtools/0.8.1-foss-2019b pycoQC/2.5.0.21-foss-2019b-Python-3.7.4 pyDNase/0.3.0-foss-2019b-Python-3.7.4

Other Versions

These versions of Pysam 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
0.20.0-GCC-11.3.0	2022a
0.19.1-GCC-11.3.0	2022a
0.18.0-GCC-11.2.0	2021b
0.17.0-GCC-11.2.0	2021b
0.16.0.1-GCC-10.3.0	2021a
0.16.0.1-GCC-9.3.0	2020a
0.15.2-fosscuda-2019a	2019a
0.15.2-foss-2019a	2019a
0.15.1-foss-2018b-Python-3.6.6	2018b
0.15.1-foss-2018b-Python-2.7.15	2018b
0.13-foss-2018b-Python-3.6.6	2018b

Last modified on 28th April 2020