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assorded packaging improvements

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commit 931db5983c74e8209f43fcf26f3f5c8857821bb8 1 parent 0a3b1a3
@ryneches authored
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1  MANIFEST.in
@@ -0,0 +1 @@
+include README
View
44 README
@@ -24,14 +24,47 @@ nice.
$ cd ~
$ virtualenv --system-site-packages opt
$ PATH=~/opt/bin:$PATH
- $ pip install numpy # install prerequisites
- $ pip install scipy # install prerequisites
- $ pip install cython # install prerequisites
- $ pip install matplotlib # install prerequisites
- $ pip install pysam # install prerequisites
+ $ pip install numpy # prerequisite
+ $ pip install scipy # prerequisite
+ $ pip install cython # prerequisite
+ $ pip install matplotlib # prerequisite
+ $ pip install pysam # prerequisite
+ $ pip install argcomplete # suggested package
+ $ pip install ipython # suggested package
$ pip install pique # install Pique
$ pique test
+If you are running Debian or Ubuntu, we recommend using apt-get for
+most of the prerequisites.
+
+ $ sudo apt-get install python-numpy \
+ python-scipy \
+ python-matplotlib \
+ python-virtualenv \
+ cython \
+ ipython
+ $ cd ~
+ $ virtualenv --system-site-packages opt
+ $ PATH=~/opt/bin:$PATH
+ $ pip install pysam
+ $ pip install argcomplete
+ $ pip install pique
+ $ pique test
+
+In your .bashrc file, we suggest adding ~/opt/bin to your PATH :
+
+ $ cd ~
+ $ cat >> .bashrc
+ PATH=~/opt/bin:$PATH
+ export PATH
+ [ctrl-D]
+
+If you installed argcomplete, you can enable tab completion for pique
+commands by placing this into your .bashrc :
+
+ eval "$(register-python-argcomplete pique)"
+
+
TESTING DATA
------------
@@ -85,6 +118,7 @@ Suggested :
ipython
samtools
+ argcomplete
Gaggle Genome Browser
USAGE
View
2  pique/fileIO.py
@@ -28,7 +28,7 @@ def downloadURL( url, path ) :
file_path = os.path.join( path, file )
meta = u.info()
- file_size = int(meta.getheaders("Content-Length")[0])
+ file_size = int(meta.getheader("Content-Length"))
# if we've already downloaded the file, don't download it again
if os.path.isfile( file_path ) :
View
10 pique/tests/__init__.py
@@ -2,19 +2,19 @@
nose tests for pique.
"""
import pique.data
+import pique.constants
import numpy
def test_init_PiqueData() :
# does the data load?
- D = pique.data.PiqueData( 'data/IP.bam', 'data/WCE.bam', 'data/map.gff', name='test' )
-
- # did we get the expected number of contigs?
- assert len( D.data.keys() ) == 3
+ D = pique.data.PiqueData( pique.constants.test_ip_file, \
+ pique.constants.test_bg_file, \
+ pique.constants.test_map_file, \
+ name='test' )
# are they the ones we were looking for?
assert D.data.keys().__contains__( 'Chromosome' )
- assert D.data.keys().__contains__( 'PNRC100' )
assert D.data.keys().__contains__( 'PNRC200' )
# is the track data present?
View
9 setup.py
@@ -11,19 +11,16 @@
Extension( 'pique.peak' , [ 'pique/peak.pyx' ] ) ]
setup(name = 'pique',
- version = '0.1',
+ version = '0.1.1',
description = 'An efficient peak finder for high coverage ChIP-seq experiments.',
#long_description=read('README'),
author = 'Russell Neches',
author_email = 'ryneches@ucdavis.edu',
url = 'https://github.com/ryneches/pique',
- packages = ['pique', 'pique.tests'],
- package_data = {'pique.tests': ['test_IP_fwd.txt', \
- 'test_IP_rev.txt', \
- 'test_WCE_fwd.txt', \
- 'test_WCE_rev.txt' ]},
+ packages = [ 'pique' ],
license = 'BSD',
test_suite = 'nose.collector',
+ tests_require=['nose'],
cmdclass = { 'build_ext' : build_ext },
ext_modules = ext_modules,
classifiers = [
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