ConradStack

#!/usr/bin/env python3

import argparse
import os
import sys

# Deinterlace an interlaced fastq file 
# (modified from iamdelf/deinterlace)

# usage: 

ConradStack

// Use Gists to store code you would like to remember later on
console.log(window); // log the "window" object to the console

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#!/bin/bash

## Tested and worked on Mac OSX 10.11

# Download bedtools2 from github:
wget https://github.com/arq5x/bedtools2/releases/download/v2.25.0/bedtools-2.25.0.tar.gz

# unzip, navigate, and build
tar -zxvf bedtools-2.25.0.tar.gz
cd bedtools2/

ConradStack

# Template for ~/.Rprofile script

# environmental variables:
Sys.setenv(
	AUTHOR="Conrad Stack",
	EMAIL="conrad.stack@someserver.com"
)

# options():
options("stringsAsFactors"=FALSE)

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##
## From http://www.r-bloggers.com/adding-metadata-to-variables/
## 

# add a comment to a variable (NB -> comment(...) function is base R)
# example
xx <- 1:10
comment(xx) <- "one through ten"
attributes(xx) 
comment(xx) <- "another one"  # NB -> adding another comment overwrites the last one

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# Steps:
# 1. Install prerequisite R packages (devtools, BSgenome)
# 2. Install BSgenome.Tcacao packages from github

### install devtools (if needed)
install.packages("devtools")

### install BSgenome from bioconductor
source("https://bioconductor.org/biocLite.R")
biocLite("BSgenome")

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require(RCurl)
require(XML)
require(stringr)

pull.to = "~/tmp"
misc.dir = sprintf("%s/lectures",pull.to)
base.url = "http://www.stat.cmu.edu/~cshalizi/uADA/15/"
lns = readLines(base.url)
top = grep("<h2>schedule",lns,ignore.case=T)
use = lns[top:length(lns)]