Merge pull request #7 from shenwei356/master

fix the ambiguity problem of package name "recycle" and script "recycle.py"
Shamir-Lab · Feb 25, 2017 · 48ea5b5 · 48ea5b5
2 parents d45ef37 + 3e643ef
commit 48ea5b5
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Showing 10 changed files with 9 additions and 6 deletions.
diff --git a/.gitignore b/.gitignore
@@ -1,2 +1,4 @@
 test/*bam
 test/*bam.bai
+*.pyc
+*.directory
diff --git a/README.md b/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

diff --git a/bin/make_fasta_from_fastg.py b/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(

diff --git a/bin/recycle.py b/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():

diff --git a/recycle/__init__.pyc b/recycle/__init__.pyc
diff --git a/recycle/run.pyc b/recycle/run.pyc
diff --git a/recycle/utils.pyc b/recycle/utils.pyc
diff --git a/recycle/__init__.py → recyclelib/__init__.py b/recycle/__init__.py → recyclelib/__init__.py
diff --git a/recycle/utils.py → recyclelib/utils.py b/recycle/utils.py → recyclelib/utils.py
diff --git a/setup.py b/setup.py
@@ -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',