If you want to do the direct pip installation, you can grab the config files from the repository and place them in whatever directory you want to execute from, or set the LUIGI_CONFIG_PATH environmental variable to point to their location. Pip install -e Comparative-Annotation-Toolkit
In the meantime, you may be better off instead cloning the directory and installing from your clone: I am still trying to figure out how to approach this problem. However, at this time, direct pip installation will mean that the luigi.cfg, logging.cfg, and test files will be buried in your python directory. The pipeline can be installed by a simple pip install: Memory usage is moderate.Ībove is a flowchart schematic of the functionality of the CAT pipeline. For full runs on many genomes, a decent amount of computational effort is required. This pipeline is capable of running both on local cluster hardware as well as on common cloud infrastructure using the toil workflow engine.
This project aims to provide a straightforward end-to-end pipeline that takes as input a HAL-format multiple whole genome alignment as well as a GFF3 file representing annotations on one high quality assembly in the HAL alignment, and produces a output GFF3 annotation on all target genomes chosen.
