Script to run the BLAST step included in OrthoFinder on a cluster (OGE)
Python
Switch branches/tags
Nothing to show
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Failed to load latest commit information.
.gitignore
README.md
blast_on_cluster.py

README.md

blastp_on_cluster

Script to run the BLAST step included in OrthoFinder on a cluster (OGE)

How it works

You need to run OrthoFinder using the -op option, to only prepare the blast files. At the end OrthoFinder will print the required blastp commands to the screen. This script will catch those commands and submit them as individual jobs (multi-threaded).

As such the clusters scheduler and queue is used, which is much more efficient than the one included in OrthoFinder. Also this allows the BLAST to run on multiple machines simultaniously.

Usage

orthofinder.py -f <FASTA_DIR> -op | python3 blast_on_cluster.py

Once the cluster is done performing all the BLASTs your should resume OrthoFinder using the command below

orthofinder.py -b <BLAST_DIR>

Todo

  • Replace hard-coded stuff (like name of the blast module and number of threads) with arguments