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Installation

Custom installation

Dictys depends on several softwares. There are often multiple methods to install each software if one method fails.

  • For bedtools, homer, samtools, macs2, and ffmpeg, you can install them through conda, module add, or manually.
  • For pytorch, you can use any supported method for your computing platform.
  • For dictys and its pypi dependencies, you can install with pip install git+https://github.com/pinellolab/dictys.git
  • For upgrading matplotlib, you need to uninstall pyDNase first, upgrade matplotlib, and then reinstall pyDNase ignoring its dependencies.

You can also use precompiled docker or singularity containers (TBA).

Dictys relies on pytorch for GPU capacity. To enable GPU support, simply install pytorch with GPU support.

Issues

Please raise an issue on github if none of the above works.