Imporved description for installation in README.md

README.md

@@ -7,38 +7,16 @@ For further information read the [documentation](https://github.molgen.mpg.de/lo
 ## Dependencies
 * [conda](https://conda.io/docs/user-guide/install/linux.html)
 * [Nextflow](https://www.nextflow.io/)
-* [MEME-Suite](http://meme-suite.org/doc/install.html?man_type=web)
 
 ## Installation
-Start with installing all dependencies listed above. It is required to set the [enviroment paths for meme-suite](http://meme-suite.org/doc/install.html?man_type=web#installingtar).
-this can be done with following commands:
-```
-export PATH=[meme-suite instalation path]/libexec/meme-[meme-suite version]:$PATH
-export PATH=[meme-suite instalation path]/bin:$PATH
-```
-
+Start with installing all dependencies listed above (Nextflow, conda) and downloading all files from the [GitHub repository](https://github.molgen.mpg.de/loosolab/masterJLU2018).
 
-Download all files from the [GitHub repository](https://github.molgen.mpg.de/loosolab/masterJLU2018).
-The Nextflow-script needs a conda enviroment to run. Nextflow can create the needed enviroment from the given yaml-file.
-On some systems Nextflow exits the run with following error:
-```
-Caused by:
-  Failed to create Conda environment
-  command: conda env create --prefix  --file env.yml
-  status : 143
-  message:
-```
-If this error occurs you have to create the enviroment before starting the pipeline.
-To create this enviroment you need the yml-file from the repository.
-Run the following commands to create the enviroment:
-```console
-path=[Path to given masterenv.yml file]
-conda env create --name masterenv -f=$path
-```
-When the enviroment is created, set the variable 'path_env' in the configuration file as the path to it.
+Every other dependency will be automatically  installed by Nextflow using conda. For that a new conda enviroment will be created, which can be found in the from Nextflow created work directory after the first pipeline run. 
+It is **not** required to create and activate the enviroment from the yaml-file beforehand.
 
 **Important Note:** For conda the channel bioconda needs to be set as highest priority! This is required due to two differnt packages with the same name in different channels. For the pipeline the package jellyfish from the channel bioconda is needed and **NOT** the jellyfisch package from the channel conda-forge!
 
+
 ## Quick Start
 ```console
 nextflow run pipeline.nf --bigwig [BigWig-file] --bed [BED-file] --genome_fasta [FASTA-file] --motif_db [MEME-file] --config [UROPA-config-file]
@@ -105,6 +83,24 @@ Optional arguments:
 All arguments can be set in the configuration files
  ```
 
+For further information read the [documentation](https://github.molgen.mpg.de/loosolab/masterJLU2018/wiki)
 
+## Known issues
+The Nextflow-script needs a conda enviroment to run. Nextflow creates the needed enviroment from the given yaml-file.
+On some systems Nextflow exits the run with following error:
+```
+Caused by:
+  Failed to create Conda environment
+  command: conda env create --prefix  --file env.yml
+  status : 143
+  message:
+```
+If this error occurs you have to create the enviroment before starting the pipeline.
+To create this enviroment you need the yml-file from the repository.
+Run the following commands to create the enviroment:
+```console
+path=[Path to given masterenv.yml file]
+conda env create --name masterenv -f $path
+```
+When the enviroment is created, set the variable 'path_env' in the configuration file as the path to it.
 
-For further information read the [documentation](https://github.molgen.mpg.de/loosolab/masterJLU2018/wiki)