From fee59c28a61b2150d5ef456742d2f67147b7fc20 Mon Sep 17 00:00:00 2001
From: Rahul Pisupati <rahul.pisupati@gmi.oeaw.ac.at>
Date: Fri, 1 Sep 2017 14:22:00 +0200
Subject: [PATCH] installation issues

---
 README.md                 | 13 ++++---------
 setup.py                  |  1 -
 snpmatch/core/snpmatch.py |  2 +-
 3 files changed, 5 insertions(+), 11 deletions(-)

diff --git a/README.md b/README.md
index 928ff08..17d9ebf 100644
--- a/README.md
+++ b/README.md
@@ -6,22 +6,17 @@ SNPmatch is a Python toolkit which can be used to genotype a sample from as-low-
 
 The below steps deal with running SNPmatch on a local machine. This package is only tested in Python 2.
 
-### Dependencies
-The SNPmatch uses various python packages (Cython, numpy, pandas, [PyGWAS](https://github.com/timeu/PyGWAS), scikit-allel). Most of which are automatically downloaded and installed with pip. Cython has to be installed before hand as given below.
-```bash
-pip install Cython
-```
-
-### Installation using pip:
+### Installation using pip
 
-SNPmatch can be easily installed with the help of pip. It can be installed from the git repo or through PyPi. The requried pip commands are given below.
+SNPmatch can be easily installed with the help of pip. SNPmatch uses various python packages (numpy, pandas, [PyGWAS](https://github.com/timeu/PyGWAS), [scikit-allel](https://github.com/cggh/scikit-allel)), which are automatically downloaded and installed while using pip. Follow the commands below for successful installation.
 
 ```bash
 ## installing SNPmatch from git hub repository
-pip install -e git+https://github.com/Gregor-Mendel-Institute/SNPmatch.git
+pip install git+https://github.com/Gregor-Mendel-Institute/SNPmatch.git
 ## or PyPi
 pip install SNPmatch
 ```
+SNPmatch can be installed either from the git repo or through PyPi.
 
 ### Database files
 
diff --git a/setup.py b/setup.py
index d6b789d..089b6b9 100644
--- a/setup.py
+++ b/setup.py
@@ -26,7 +26,6 @@
     keywords='Genotyping Low Coverage sequencing data',
     packages=find_packages(exclude=['contrib', 'docs', 'tests*']),
     install_requires=[
-        "Cython",
         "scipy >= 0.17.0",
         "numpy >=1.9.0",
         "PyGWAS",
diff --git a/snpmatch/core/snpmatch.py b/snpmatch/core/snpmatch.py
index f4976d4..d51b0e5 100644
--- a/snpmatch/core/snpmatch.py
+++ b/snpmatch/core/snpmatch.py
@@ -199,7 +199,7 @@ def parseInput(inFile, logDebug, outFile = "parser"):
                 DPmean = "NA"
             else:
                 die("input file type %s not supported" % inType)
-            log.info("creating snpmatch parser file: %s", outFile)
+            log.info("creating snpmatch parser file: %s", outFile + '.npz')
             np.savez(outFile, chr = snpCHR, pos = snpPOS, gt = snpGT, wei = snpWEI, dp = DPmean)
             NumSNPs = len(snpCHR)
             case = 0