stephenturner

## See http://gettinggeneticsdone.blogspot.com/2013/06/customize-rprofile.html

## Load packages
library(BiocInstaller)

## Don't show those silly significanct stars
options(show.signif.stars=FALSE)

## Do you want to automatically convert strings to factor variables in a data.frame?
## WARNING!!! This makes your code less portable/reproducible.

cobyism

Deploying a subfolder to GitHub Pages

Sometimes you want to have a subdirectory on the master branch be the root directory of a repository’s gh-pages branch. This is useful for things like sites developed with Yeoman, or if you have a Jekyll site contained in the master branch alongside the rest of your code.

For the sake of this example, let’s pretend the subfolder containing your site is named dist.

Step 1

Remove the dist directory from the project’s .gitignore file (it’s ignored by default by Yeoman).

nickloman

rsync -av rsync://ftp.ncbi.nlm.nih.gov/genomes/Bacteria --include "*/" --include "Bacteria/Escherichia*/*.fna" --exclude=* .

# bonus script - concatenate chromosomes and plasmids into single fasta file, make sure the files don't already exist

find . -mindepth 1 -type d | xargs -L 1 -I '{}' find {} -name "*.fna" | while read i ; do cat "$i" >> `dirname "$i"`.fasta ; done

henrik

tmux cheatsheet

As configured in my dotfiles.

start new:

tmux

start new with session name:

jimbojsb

Step 0:

Get Homebrew installed on your mac if you don't already have it

Step 1:

Install highlight. "brew install highlight". (This brings down Lua and Boost as well)

Step 2: