Ecvotools. Ecology and Evolution Tools.

Description

Set of different tools for ecology and evolution analysis.

Contents

src/multiblast.py . Multi-core blast. Snakemake workflow.
src/multiblast_slurm.py . Multi-core blast on slurm. Snakemake workflow.
data/*fasta. Fasta files to perform an example run using multiblast/multiblast_slrum scripts.

multiblast.py - multiblast_slurm.py

Speed up a blast run, trimming the query fasta file and running it on multiple cores/nodes with multi-threads.

Usage

(dry run) $ snakemake --snakefile multiblast.py --config fadb=base.fasta faqy=query.fasta dbtype=nucl -j 4 -np

or, in a cluster with slurm:

(dry run) $ snakemake --snakefile multiblast_slurm.py --config fadb=base.fasta faqy=query.fasta dbtype=nucl -j 999 --cluster-config cluster.json --cluster "sbatch -c {cluster.cpus-per-task} -p {cluster.partition} -t {cluster.time} --mem {cluster.mem}" -np

A config file for snakemake is included (cluster.json)