Small changes

Author: jfnavarro

README.md

@@ -14,7 +14,7 @@ The ST Pipeline has been optimized for speed, robustness and it is very easy to
 The following files/parameters are required :
 - FASTQ files (Read 1 containing the spatial information and the UMI and read 2 containing the genomic sequence) 
 - A genome index generated with STAR 
-- An annotation file in GTF or GFF format
+- An annotation file in GTF or GFF3 format
 - The file containing the barcodes and array coordinates (look at the folder "ids" and chose the correct one). Basically this file contains 3 columns (BARCODE, X and Y), so if you provide this file with barcodes identinfying cells (for example), the ST pipeline can be used for single cell data.
 - A name for the dataset
 
@@ -122,9 +122,11 @@ The ST pipeline is open source under the MIT license which means that you can us
 
 **Reference**
 
-If you use the ST Pipeline, please refer to it by including this:
+If you use the ST Pipeline, please refer its publication: 
 
-TODO: add reference
+ST Pipeline: An automated pipeline for spatial mapping of unique transcripts
+Oxford BioInformatics
+10.1093/bioinformatics/btx211
 
 **Contact**
 

setup.py

@@ -1,10 +1,11 @@
 #!/usr/bin/python
 """
-ST Pipeline is a tool to process the Spatial Transcriptomics raw data.
+ST Pipeline is a tool to process Spatial Transcriptomics raw data (or 
+any type of single cell data whose raw data has the same configuraiton).
 The data is filtered, aligned to a genome, annotated to a reference,
 demultiplexed by array coordinates and then aggregated by counts
-that are not duplicates using the Unique Molecular Indentifiers. 
-The output contains the counts table, a stats file, a log file
+that are not duplicates using the Unique Molecular Indentifiers (UMIs). 
+The output contains a counts table, a stats file, a log file
 and a BED file with all the transcripts.
 """
 
@@ -14,7 +15,10 @@
 import sys
 from setuptools import setup, find_packages
 from stpipeline.version import version_number
-from Cython.Build import cythonize
+try:
+    from Cython.Build import cythonize
+except ImportError:
+    raise SystemExit("ST Pipeline requires Cython")
 
 # Get the long description from the relevant file
 here = os.path.abspath(os.path.dirname(__file__))
@@ -27,7 +31,6 @@
 except IOError:
     install_requires = []
 
-
 major, minor1, minor2, s, tmp = sys.version_info
 if major != 2 or minor1 < 7:
     raise SystemExit("ST Pipeline requires Python 2.7.x")