Make rose2 python3 compatible and a callable python function

CHANGELOG.rst

@@ -0,0 +1,12 @@
+##########
+Change Log
+##########
+
+All notable changes to this project are documented in this file.
+
+
+Added
+-----
+- Make ``rose2`` python3 compatible
+- Make ``rose2`` a callable python function
+

LICENSE.txt

@@ -1,6 +1,6 @@
 The MIT License (MIT)
 
-Copyright (c) 2014 Charles Lin (Bradner Lab)
+Copyright (c) 2018 Charles Lin (Bradner Lab)
     and Collaborators:
         John DiMatteo
         Nick Semenkovich | semenko@alum.mit.edu | https://nick.semenkovich.com
@@ -21,4 +21,4 @@ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
 FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
 COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
 IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
-CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

MANIFEST.in

@@ -1,2 +1,2 @@
 include README.md
-recursive-include annotation * 
+recursive-include rose2/annotation *

README.md

@@ -8,10 +8,29 @@ Install
 =======
 
 ```
-pip install -e git+https://github.com/linlabbcm/rose2.git#egg=rose2
+pip install -e git+https://github.com/linlabbcm/rose2.git
 ```
 
 Dependencies
 ============
 
-ROSE 2 requires [Bamliquidator](https://github.com/BradnerLab/pipeline/wiki/bamliquidator).
+The CRC software uses the following dependencies:
+
+- ``Bamliquidator``
+
+- ``Samtools``
+
+Usage
+=====
+
+As a command line tool:
+```
+rose2 -g [GENOME] -i [INPUT_REGION_GFF] -r [RANKBY_BAM_FILE] -o [OUTPUT_FOLDER] [OPTIONAL_FLAGS]
+```
+
+As a python library:
+```
+import rose2
+
+rose2.rose(input_file, rankby, output_folder, genome, bams=None, control='', stitch=None, tss=0, mask_file=None)
+```