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#/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 $PREFIX | |
fi |
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from __future__ import print_function | |
from functools import wraps | |
class UnitialisedFunctionCallException(Exception): | |
pass | |
def setup_function(function_): | |
@wraps(function_) | |
def setter(self, *args, **kwargs): |
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#/bin/bash | |
# Get installation prefix from the args | |
PREFIX=$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 |
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#!/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. |
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# 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" |
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#!/bin/bash | |
qstat -u '*' -ext |
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from rpy2.robjects import pandas2ri | |
from rpy2.robjects.packages import importr | |
import rpy2.robjects | |
import fa2 | |
import gc | |
import pandas as pd | |
import numpy as np |
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