kogakure

*.acn
*.acr
*.alg
*.aux
*.bak
*.bbl
*.bcf
*.blg
*.brf
*.bst

ijt

package main

import (
        "fmt"
        "io"
        "log"
        "net/http"
        "os"
)

seandavi

#!/bin/bash
#
# Author: Sean Davis <seandavi@gmail.com>
#
# Uses named pipes (FIFO) to reduce storage needs
# to call varscan somatic
# Some details may need to be edited to meet particular needs
# call with the following parameters
# 1) The FASTA file containing the reference genome
# 2) The Normal bam file

obeattie

#!/usr/bin/env python
import optparse
import sys

from boto.s3.connection import S3Connection

def sign(bucket, path, access_key, secret_key, https, expiry):
    c = S3Connection(access_key, secret_key)
    return c.generate_url(
        expires_in=long(expiry),

bkreider

"""A notebook manager that uses S3 storage. (based on the Azure manager)
http://ipython.org/ipython-doc/dev/interactive/htmlnotebook.html#using-a-different-notebook-store

Drop this file in IPython/frontend/html/notebook

1. Create a new notebook profile - ipython profile create nbserver
2. edit ~/.ipython/profile_nbserver/ipython_notebook_config.py
3. Add these lines:

    c.NotebookApp.notebook_manager_class = 'IPython.frontend.html.notebook.s3nbmanager.S3NotebookManager'

ogrrd

Never touch your local /etc/hosts file in OS X again

To setup your computer to work with *.test domains, e.g. project.test, awesome.test and so on, without having to add to your hosts file each time.

Requirements

• Homebrew
• Mountain Lion -> High Sierra

Install

hadley

Notes:

• I've tried to break up in to separate pieces, but it's not always possible: e.g. knowledge of data structures and subsetting are tidy intertwined.

• Level of Bloom's taxonomy listed in square brackets, e.g. http://bit.ly/15gqPEx. Few categories currently assess components higher in the taxonomy.

Programming R curriculum

Data structures

sloria

The Best of the Best Practices (BOBP) Guide for Python

A "Best of the Best Practices" (BOBP) guide to developing in Python.

In General

Values

• "Build tools for others that you want to be built for you." - Kenneth Reitz
• "Simplicity is alway better than functionality." - Pieter Hintjens

rmflight

#!/path/2/Rscript

# License: CC0 (just be nice and point others to where you got this)
# Author: Robert M Flight <rflight79@gmail.com>, github.com/rmflight
#
# This is a post-commit hook that after a successful commit subsequently increments the package version in DESCRIPTION
# and commits that. Analogous to the pre-commit at https://gist.github.com/rmflight/8863882, but useful if you only have
# good reasons for not doing it on the pre-commit.
#
# To install it, simply copy this into the ".git/hooks/post-commit" file of your git repo, change /path/2/Rscript, and make

jcaddel

Install s3fs on Mac OS X

1 - Install Homebrew - http://brew.sh/
  ruby -e "$(curl -fsSL https://raw.github.com/Homebrew/homebrew/go/install)"
  
2 - Use Homebrew to install s3fs + dependencies
  brew install s3fs
  
3 - Do some custom stuff.  I only used the first step from here -> https://gist.github.com/fukayatsu/3910097
  sudo /bin/cp -rfX /usr/local/Cellar/fuse4x-kext/0.9.2/Library/Extensions/fuse4x.kext /Library/Extensions