update README and use markdown

README.md

+# Je
+
+Additional documentation and support can be found at http://gbcs.embl.de/je
+
+## Installation
+
+* Install from the bioconda channel with `` conda install -c bioconda je-suite ``
+* Or, download the ``je_<version>.tar.gz`` from the ``dist/`` directory and unpack
+
+## The Je tool suite
+
+Je currently offers 4 tools:
+
+* **je clip**
+
+	to remove UMIs contained in reads of fastq files that do not need sample demultiplexing
+
+* **je demultiplex**
+
+	to demultiplex multi-samples fastq files which reads contain barcodes and UMIs (or not)
+
+* **je demultiplex-illu**
+
+ 	to demultiplex fastq files according to associated index files (contain the sample encoding barcodes).
+ 	Reads can additionally contain UMIs (inline)
+
+* **je markdupes**
+
+ 	to filter BAM files for read duplicates taking UMIs into account
+
+
+### Distributions
+
+* ``dist/``
+
+    contains the different Je versions for download
+
+* Bioconda
+
+	starting from version 1.2 je-suite can be installed through conda: https://anaconda.org/bioconda/je-suite
+
+### Source
+
+* ``src/shell/je``
+
+    is the wrapper script to call ``java -jar je_1.0_bundle.jar``
+
+* ``src/galaxy/``
+
+    contains the Je wrappers for Galaxy
+
+* ``src/test/``
+
+    holds the different test data

README.rst

-Je
---
-
-Additional documentation and support can be found at http://gbcs.embl.de/je
-
-
-The Je tool suite
-=================
-
-Contains
-++++++++
-Je currently offers 4 tools :
-
-  **je clip**
-
-    to remove UMIs contained in reads of fastq files that do not need sample demultiplexing
-
-  **je demultiplex**
-
-    to demultiplex multi-samples fastq files which reads contain barcodes and UMIs (or not)
-
-  **je demultiplex-illu**
-
-     to demultiplex fastq files according to associated index files (contain the sample encoding barcodes).
-     Reads can additionally contain UMIs (inline)
-
-  **je markdupes**
-
-     to filter BAM files for read duplicates taking UMIs into account
-
-
-Distributions
-++++++
-dist/
-    contains the different Je versions for download 
-
-Source
-++++++
-
-src/shell/je
-    is the wrapper script to call ``java -jar je_1.0_bundle.jar``
-
-src/galaxy/
-    contains the Je wrappers for Galaxy
-
-src/test/
-    holds the different test data
\ No newline at end of file