Added support for MethylationEPIC assays

README.md

@@ -1,7 +1,7 @@
 ADMIRE - Analysis of DNA methylation in genomic regions
 =======================================================
 
-ADMIRE is a semi-automatic analysis pipeline and visualization tool for Infinium HumanMethylation450K Chips.
+ADMIRE is a semi-automatic analysis pipeline and visualization tool for Infinium HumanMethylation450K and Infinium MethylationEpic assays.
 
 Use ADMIRE online: https://bioinformatics.mpi-bn.mpg.de
 
@@ -24,20 +24,27 @@ We have a extensive documentation with a use case available [here](http://admire
 Installation and Command-line usage
 -----------------------------------
 
-Make sure all prerequisites are met:
+We recommend to install prerequisites using the conda package manager. Make sure to have `conda` installed, e.g. via
 
-* [comb-p](https://github.com/brentp/combined-pvalues)
-* [bedtools](https://github.com/arq5x/bedtools2)
-* [R/Rscript](http://www.r-project.org/)
-* [python - numpy](http://continuum.io/downloads)
-* [python - matplotlib](http://continuum.io/downloads)
+- [Miniconda](https://conda.io/miniconda.html)
+	- download the Miniconda installer for **Python 3**
+	- run ```bash Miniconda3-latest-Linux-x86_64.sh``` to install Miniconda
+	- Answer the question "Do you wish the installer to prepend the Miniconda install location to PATH in your /home/.../.bashrc ?" with yes
+		OR do ```PATH=dir/to/miniconda3:$PATH``` after installation process
 
-Install admire locally by running:
+Clone the ADMIRE repository and populate an environment with all prerequisites:
 
-    git clone https://github.molgen.mpg.de/loosolab/admire
-    export PATH=$PATH:dir/to/admire/src
+```bash
+$ git clone https://github.molgen.mpg.de/loosolab/admire
+$ conda env create -f admire/environment.yaml
+$ export PATH=$PATH:dir/to/admire/src
+```
+
+Every time you intent to use ADMIRE, make sure the environment is activated:
 
 ```bash
+$ source activate admire
+$ admire -h
 Usage: admire [options]
 
 Available options: