ConradStack

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)]

ConradStack

# 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")

ConradStack

##
## 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

ConradStack

# Template for ~/.Rprofile script

# environmental variables:
Sys.setenv(
	AUTHOR="Conrad Stack",
	EMAIL="[email protected]"
)

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

ConradStack

#!/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

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

ConradStack

#!/usr/bin/env python3

import argparse
import os
import sys

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

# usage: 

ConradStack

import(rtracklayer)

# Where syn is a list of GRanges objects:
test = GenomicRangesList(syn)
export.gff(test,"~/tmp/tmp.gff3", version="3")

# ... or a single GRanges element:
export.gff(syn[[1]],"~/tmp/tmp.gff3", version="3")

ConradStack

## If python 3.5, say, has been installed but you want to use v2.7 for 
## a particular project

# Create environment for different (or specific) version of python:
conda create -n py27 python=2.7 anaconda

# Check available environments (optional)
# conda info --envs

ConradStack

#!/bin/bash
# From: http://www.cyberciti.biz/faq/exclude-certain-files-when-creating-a-tarball-using-tar-command/

tar --exclude-vcs --exclude='nohup.out' -cjf ~/tmp/whatever.tar.bz2 ./*