TOBIAS 0.13.3-foss-2021b

TOBIAS is a collection of command-line bioinformatics tools for performing footprinting analysis on ATAC-seq data, and includes: Correction of Tn5 insertion bias; Calculation of footprint scores within regulatory regions; Estimation of bound/unbound transcription factor binding sites; and Visualization of footprints within and across different conditions

Accessing TOBIAS 0.13.3-foss-2021b

To load the module for TOBIAS 0.13.3-foss-2021b please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):

module load bear-apps/2021b
module load TOBIAS/0.13.3-foss-2021b

BEAR Apps Version

2021b

Architectures

EL8-cascadelake — EL8-haswell — EL8-icelake — 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.

Extensions

  • configs 3.0.3
  • kneed 0.7.0
  • logomaker 0.8
  • MOODS-python-1.9.4.1
  • PyPDF2 1.26.0
  • reportlab 3.6.2
  • statistics 1.0.3.5
  • svist4get 1.2.24
  • TOBIAS 0.13.3
  • Wand 0.6.7

More Information

For more information visit the TOBIAS website.

Dependencies

This version of TOBIAS has a direct dependency on: adjustText/0.7.3-foss-2021b Biopython/1.79-foss-2021b boto3/1.20.13-GCCcore-11.2.0 foss/2021b ImageMagick/7.1.0-4-GCCcore-11.2.0 pybedtools/0.8.2-GCC-11.2.0 pyBigWig/0.3.18-foss-2021b Pysam/0.17.0-GCC-11.2.0 Python/3.9.6-GCCcore-11.2.0 PyYAML/5.4.1-GCCcore-11.2.0 scikit-learn/1.0.1-foss-2021b SciPy-bundle/2021.10-foss-2021b Seaborn/0.11.2-foss-2021b XlsxWriter/3.0.2-GCCcore-11.2.0

Last modified on 23rd August 2022