updated docs (added command for new helper script)

README.md

@@ -9,7 +9,8 @@ automatically.
   * Support for [PBS](https://en.wikipedia.org/wiki/Portable_Batch_System) / [Torque](http://www.adaptivecomputing.com/products/open-source/torque/) scheduler (note proper [configuration](./docs/configuration.md) is required)
   * [HISAT2](https://ccb.jhu.edu/software/hisat2/index.shtml) can be used as an alternative to [BowTie2](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml) and [TopHat 2](https://ccb.jhu.edu/software/tophat/index.shtml)
   * Added [helper](./docs/helper.md) script to do PCA on samples
-  * **Parameter names in data.ini changed**
+  * **Parameter names in data.ini changed, additional options added to config.ini**. Check the [configuration](./docs/configuration.md)
+   and update the files accordingly.
 
 ## Workflow
 

config.template.ini

@@ -91,7 +91,7 @@ samtools_module=biotools/samtools-1.3
 sratoolkit_module=biotools/sratoolkit-2.5.7
 tophat_module=biotools/tophat-2.1.0
 
-hisat2_module=
+hisat2_module=biotools/hisat2-2.1.0
 
 interproscan_module=biotools/interproscan-5.16-55.0
 

docs/configuration.md

@@ -1,18 +1,9 @@
 # Configuring LSTrAP
 ## config.ini
-In your config file module names need to be specified. To see which modules are available on your system type:
-
-    module avail
-
-Add the module name for each of the tools to your config.ini, also update all paths (!) e.g. Trimmomatic.
-In case the module load system isn't used, but all software is installed on the cluster + nodes set the modules to **None** !
-
-In case you would like to tweak parameters passed to tools this would be the place to do so. Note however that the tools
-will run with the same settings for each file. Modifying parameters that would **change the output name or format will 
-cause the pipeline to break**. Arguments with a name like *${var}* should **not** be changed as this is how the pipeline 
-defines the input and output for each tool.
+Before running LSTrAP make sure **all paths in config.ini match your system's setup**, e.g. Trimmomatic adapters and jar will 
+need to be adapted.
 
-**Paths** will differ on your system, make sure to set these up correctly
+### qsub parameters
 
 Additional parameters can be added to the qsub commands at the bottom, 
 this allows users to submit jobs to specific queues, with specific 
@@ -27,6 +18,22 @@ starting TopHat with **-p 3** the job will require 4 cores (3 worker
 threads and a background thread are active when a job is started this 
 way).
 
+### Environment modules
+In case the module load system isn't used, but all software is installed on the cluster + nodes set the modules to **None** !
+
+In your config file module names need to be specified. To see which modules are available on your system type:
+
+    module avail
+
+Add the module name for each of the tools to your config.ini if your system is using environmental modules.
+
+### Tweaking parameters of individual tools (expert feature)
+
+In case you would like to tweak parameters passed to tools this would be the place to do so. Note however that the tools
+will run with the same settings for each file. Modifying parameters that would **change the output name or format will 
+cause the pipeline to break**. Arguments with a name like *${var}* should **not** be changed as this is how the pipeline 
+defines the input and output for each tool.
+
 Example config.ini:
 
 ```ini

docs/preparation.md

@@ -1,6 +1,6 @@
 # Preparing your system
 
-LSTrAP is designed with High Performance Computing in mind and requires a computer cluster running 
+LSTrAP is designed with High Performance Computing in mind and **requires** a computer cluster running 
 [Oracle Grid Engine]((https://www.oracle.com/sun/index.html)) or [PBS](https://en.wikipedia.org/wiki/Portable_Batch_System) 
 / [Torque](http://www.adaptivecomputing.com/products/open-source/torque/). Furthermore, the essential 
 tools (see below) need to be installed prior to running LSTrAP.