Merge pull request #7 from shenwei356/master

fix the ambiguity problem of package name "recycle" and script "recycle.py"

Author: rozovr

.gitignore

@@ -1,2 +1,4 @@
 test/*bam
 test/*bam.bai
+*.pyc
+*.directory

README.md

@@ -1,13 +1,14 @@
 [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square)](http://bioconda.github.io/recipes/recycler/README.html)
 
 # Getting Recycler
-You can download Recycler [here](https://github.com/Shamir-Lab/Recycler/releases/download/v0.61/Recycler-v0.61.zip) or clone it via the link below. In case you download the zip, unzip the file before following the instructions below (ignoring the 'git clone' line)
+You can download Recycler [here](https://github.com/Shamir-Lab/Recycler/releases/) or clone it via the link below. In case you download the zip, unzip the file before following the instructions below (ignoring the 'git clone' line)
 
 # Installation
 To install Recycler and scripts follow the following instructions.
 
     git clone https://github.com/rozovr/Recycler.git
-    python setup.py install
+    cd Recycler
+    python setup.py install --user
 
 
 # Quick start

bin/make_fasta_from_fastg.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 import re, argparse, os
-from recycle.utils import readfq
+from recyclelib.utils import readfq
 
 def parse_user_input():
     parser = argparse.ArgumentParser(

bin/recycle.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 
 import argparse, os
-from recycle import *
+from recyclelib.utils import *
 import pysam
 
 def parse_user_input():

recycle/__init__.pyc

@@ -1,14 +1,14 @@
 from setuptools import setup
 
 setup(name='recycler',
-      version='0.6',
+      version='0.62',
       description='Recycler: an algorithm for detecting plasmids from de novo assembly graphs',
       url='https://github.com/Shamir-Lab/Recycler',
       author='Roye Rozov',
       author_email = '',
       license='BSD-3-Clause',
       scripts = ['bin/recycle.py', 'bin/make_fasta_from_fastg.py', 'bin/get_simple_cycs.py'],
-      packages = ['recycle'],
+      packages = ['recyclelib'],
       requires=['python (<3.0)'],
       install_requires=[
         'networkx',