pritchardtom/braker_singularity

Singularity Recipe for BRAKER and all essential/optional dependencies.

BRAKER Singularity Recipe

A Singularity recipe to install BRAKER (https://github.com/Gaius-Augustus/BRAKER) and all its essential and optional dependencies.

To-Do:

...

Mandatory Deps:

• Augustus
• Bamtools
• DIAMOND

Optional Deps:

• ProHint
• Samtools
• BioPython
• GenomeThreader
• Spaln
• Exonerate
• Tools from UCSC:
  • twoBitInfo
  • faToTwoBit
• MakeHub

General:

• Check status of cpanm POSIX command.
• Check threads in Perl works okay. Tests failed due to locale issues.
• Need to export location of GeneMark-EX?

Done:

Progress.

Mandatory Deps:

• GeneMark-EX (Tested)

Optional Deps:

• Python 3.6
• cdbfasta

General:

• AUGUSTUS library dependencies installed.
• GeneMark-ES dependencies installed.