From a37b7d0cfdfcccf5ae13785af10b22f5dd7f14a1 Mon Sep 17 00:00:00 2001 From: sepro Date: Mon, 21 Nov 2016 11:53:18 +0100 Subject: [PATCH] improved docs --- README.md | 16 +++++++++++++++- 1 file changed, 15 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index ca8852f..07b6a80 100644 --- a/README.md +++ b/README.md @@ -16,7 +16,7 @@ Steps in bold are submitted to a cluster. LSTrAP is designed to run on an [Oracle Grid Engine](https://www.oracle.com/sun/index.html) computer cluster system and requires all external tools to be installed on the compute nodes. The "module load" system is supported. A comprehensive list of all tools -necessary can be found [here](docs/preparation.md) +necessary can be found [here](docs/preparation.md). Instructions to run LSTrAP on other systems are provided below. ## Installation @@ -77,6 +77,20 @@ for LSTrAP can be generated. python3 fasta_to_gtf.py /path/to/transcript.cds.fasta > output.gtf +## Adapting LSTrAP to other cluster managers + +LSTrAP is designed and tested on an Oracle Grid Engine, though with minimal effort it can be adopted to run on PBS and Torque +based systems (and likely others). First, in the configuration file, check the qsub parameters (e.g. jobs that require multiple +CPUs to run *-pe cores 4*), that differ between systems are set up properly (the nodes and cores on Torque and PBS need to be +set using *-l nodes=4:ppn=2* to request 4 nodes with 2 processes per node). + +Furthermore the submission script might differ, these are located in **./cluster/templates.py** . For PBS based systems some +settings need to be included by adding *#PBS ...*. + +We strive to get LSTrAP running on as many systems as possible. Do not hesitate to contact us in case you experience difficulties +running LSTrAP on your system. + + ## Contact LSTrAP was developped by [Sebastian Proost](mailto:proost@mpimp-golm.mpg.de) and [Marek Mutwil](mailto:mutwil@mpimp-golm.mpg.de) at the [Max-Planck Institute for Molecular Plant Physiology](http://www.mpimp-golm.mpg.de/2168/en)