lukauskas

#/bin/bash

# Get installation prefix from the args
PREFIX=$HOME # Default to home
if [ -n "$1" ]; then
    PREFIX=$1
    if [ ! -d "$PREFIX" ]; then
        mkdir $PREFIX
    fi
    PREFIX=`cd $PREFIX; pwd` # Convert to absolute path

lukauskas

lukauskas

#!/usr/bin/env python
"""
simple example script for running and testing notebooks.

Forked from shoyer / ipnbdoctest.py (https://gist.github.com/shoyer/7497853),
who has forked from the original author minrk/ipnbdoctest.py (https://gist.github.com/minrk/2620735)

Usage: `ipnbdoctest.py foo.ipynb [bar.ipynb [...]]`

Each cell is submitted to the kernel, and the outputs are compared with those stored in the notebook.

lukauskas

#!/usr/bin/env python
"""
Sets a random wallpaper on Mac OSX Mavericks.
The wallpaper is fetched from interfacelift's random page for Retina resolution
"""
import urllib2
import re
import os

# We need to pretend we are Chrome, otherwise HTTP 403 Forbidden is thrown

lukauskas

from __future__ import print_function
import libsbml
import argparse

def _parser():

    parser = argparse.ArgumentParser(description="Parse stoichiometry matrix of SBML file")
    parser.add_argument('file', metavar="filename", type=argparse.FileType('r'),
                        help="Filename of SBML file to parse")

lukauskas

#!/usr/bin/env python
"""
Sets a random wallpaper on Mac OSX Mavericks.
The wallpaper is fetched from interfacelift's random page for Retina resolution
"""
from urllib.request import Request, urlopen
import re
import os

# We need to pretend we are Chrome, otherwise HTTP 403 Forbidden is thrown

lukauskas

#/bin/bash
 
# Get installation prefix from the args
VERSION=2.7.9
PREFIX=$HOME/python${VERSION} # Default to home/python-2.7.9
if [ -n "$1" ]; then
    PREFIX=$1
    if [ ! -d "$PREFIX" ]; then
        mkdir $PREFIX
    fi

lukauskas

from __future__ import print_function
from functools import wraps

class UnitialisedFunctionCallException(Exception):
    pass

def setup_function(function_):

    @wraps(function_)
    def setter(self, *args, **kwargs):

lukauskas

lukauskas

#  This doesn't work nicely as it uses bioclite to install dependdencies
# which is why I'm not submitting it to AUR
# but it's useful if one compiles it themselves.
pkgname=phantompeakqualtools-git
pkgver=r30.b9267ea

pkgrel=1
pkgdesc="Computes quick but highly informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these assays."
arch=('i686' 'x86_64')
url="https://github.com/kundajelab/phantompeakqualtools"