brantfaircloth

# assume the following directory structure where contents of doc/ 
# and source/ are already checked into repo., with the exception 
# of the _build directory (i,e. you can check in _themes or _sources 
# or whatever else).
#
# proj/
#    source/
#    doc/

# remove doc/_build/html if present

stephenturner

# To source this file into an environment to avoid cluttering the global workspace, put this in Rprofile:
# my.env <- new.env(); sys.source("C:/PathTo/THIS_FILE.r", my.env); attach(my.env)

#-----------------------------------------------------------------------
#     Load packages, set options and cwd, set up database connection
#-----------------------------------------------------------------------

## Load packages
# require(ggplot2)  #plotting
# require(plyr)		#data manipulation

pithyless

Install Python

$ brew install readline sqlite gdbm
$ brew install python --universal --framework
$ python --version
Python 2.7

Symlinks...

djaiss

#!/usr/bin/env sh

##
# This is script with usefull tips taken from:
#   https://github.com/mathiasbynens/dotfiles/blob/master/.osx
#
# install it:
#   curl -sL https://raw.github.com/gist/2108403/hack.sh | sh
#

djaiss

<?php
$countries =
 
array(
"AF" => "Afghanistan",
"AL" => "Albania",
"DZ" => "Algeria",
"AS" => "American Samoa",
"AD" => "Andorra",
"AO" => "Angola",

piscisaureus

Locate the section for your github remote in the .git/config file. It looks like this:

[remote "origin"]
	fetch = +refs/heads/*:refs/remotes/origin/*
	url = git@github.com:joyent/node.git

Now add the line fetch = +refs/pull/*/head:refs/remotes/origin/pr/* to this section. Obviously, change the github url to match your project's URL. It ends up looking like this:

dsparks

doInstall <- TRUE  # Change to FALSE if you don't want packages installed.
toInstall <- c("ggplot2", "reshape2", "RColorBrewer")
if(doInstall){install.packages(toInstall, repos = "http://cran.us.r-project.org")}
lapply(toInstall, library, character.only = TRUE)

# Generate a random matrix
# This can be any type of numeric matrix,
# though we often see heatmaps of square correlation matrices.
nRow <- 9
nCol <- 16

gregpinero

import re
infile = 'dsim-all-chromosome-r1.3.reassembly1.updated_wsu1.fasta'

ref_count = 0
for line in open(infile,'r'):
	if line.startswith('>'):
		ref_count += 1
		print '>' + re.sub(r'[^0-9a-zA-Z_]', '', line)[:50]
	else:
		print line,

arq5x

HISTCONTROL="erasedups"
export HISTCONTROL

arq5x

#!/usr/bin/env python
import sys
from gemini import GeminiQuery

db = sys.argv[1]

# create a GeminiQery instance for the requested database
gq = GeminiQuery(db)