eifunannot

eifunannot - EI AHRD Functional Annotation Pipeline

eifunannot is a wrapper around Automated Assignment of Human Readable Descriptions (AHRD) designed for execution in an HPC cluster (SLURM) environment.

Gemy Kaithakottil, David Swarbreck

Getting Started

Prerequisites

snakemake>=5.4.0
blast v2.6.0
prinseq v0.20.3
interproscan v5.22.61
ahrd v3.3.3

Installation

First obtain the source code using

$ cd /path/to/eifunannot/${version}
$ git clone git@github.com:EI-CoreBioinformatics/eifunannot.git src
$ cd src
# checkout the specific tag you want to install
$ git checkout tags/v1.4.0

To install, simply use from your current pip environment:

$ version=1.4.0 && python setup.py bdist_wheel && pip install --prefix=/path/to/eifunannot/${version}/x86_64 -U dist/*whl

Create the wrapper

Make sure that both PATH and PYTHONPATH environments are updated for the new version

cd /ei/software/cb/bin
$ cat eifunannot-1.4.0
#!/bin/bash
tool="eifunannot/1.4.0"
location="/ei/software/cb"
echo "${tool} is sourced from ${location} location"

source python_miniconda-4.7.12_py3.7_gk

echo "Usage:"
echo "  eifunannot --help"

export PYTHONPATH=/ei/software/cb/eifunannot/1.4.0/x86_64/lib/python3.7/site-packages
export PATH=/ei/software/cb/eifunannot/1.4.0/x86_64/bin:$PATH

Run pipeline

Details to run the pipeline is provided in the wiki page