From 612086625e11cef215dc38772394649693039314 Mon Sep 17 00:00:00 2001 From: Sebastian Proost Date: Thu, 27 Apr 2017 15:17:15 +0200 Subject: [PATCH] Update README.md --- README.md | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 0da73a1..e39d200 100644 --- a/README.md +++ b/README.md @@ -3,7 +3,7 @@ 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 it will output the commands required and print them on the screen. This script will catch those commands and submit them as multi-threaded blast jobs. +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. @@ -14,3 +14,7 @@ As such the clusters scheduler and queue is used, which is much more efficient t Once the cluster is done performing all the BLASTs your should resume OrthoFinder using the command below orthofinder.py -b + +## Todo + + * Replace hard-coded stuff (like name of the blast module and number of threads) with arguments