improved docs

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)