Shaun Jackman sjackman

## qemu_osx_rpi_raspbian_jessie.sh
# Install Homebrew
/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

# Install QEMU OSX port with ARM support
brew install qemu
export QEMU=$(which qemu-system-arm)

# Dowload kernel and export location
brew install wget
wget https://github.com/dhruvvyas90/qemu-rpi-kernel/raw/master/kernel-qemu-4.4.34-jessie

## qemu_osx_rpi_raspbian_jessie.sh
# Install QEMU OSX port with ARM support
sudo port install qemu +target_arm
export QEMU=$(which qemu-system-arm)

# Dowload kernel and export location
curl -OL \
https://github.com/dhruvvyas90/qemu-rpi-kernel/blob/master/kernel-qemu-4.1.7-jessie
export RPI_KERNEL=./kernel-qemu-4.1.7-jessie

# Download filesystem and export location

## install-gcc48-linuxbrew-centos6.md

      
              1 file
            
          
              37 forks
            
          
              25 comments
            
          
              127 stars
            
          
                stephenturner
                / install-gcc48-linuxbrew-centos6.md
            
            
              Last active
              March 6, 2022 02:49
            
              
                Installing gcc 4.8 and Linuxbrew on CentOS 6
              
          
    Installing gcc 4.8 and Linuxbrew on CentOS 6

The GCC distributed with CentOS 6 is 4.4.7, which is pretty outdated. I'd like to use gcc 4.8+. Also, when trying to install Linuxbrew you run into a dependency loop where Homebrew's gcc depends on zlib, which depends on gcc. Here's how I solved the problem.
Note: Requires sudo privileges.
Resources:


http://superuser.com/a/676337/88393: Forum response on using CERN's open Scientific Linux distribution of RHEL's developer toolset.
http://linux.web.cern.ch/linux/devtoolset/: CERN's developer toolset installation instructions.


## add_mrna.lua
#!/usr/bin/env gt

function usage()
  io.stderr:write(string.format("Usage: %s <GFF annotation>\n" , arg[0]))
  os.exit(1)
end

if #arg < 1 then
  usage()
end

## slide.html
<!doctype html>
<html lang="en">
  <head>
    <meta charset="utf-8">

    <title>
      {% if page.title %}
        {{ page.title }} | {{ site.title }}
      {% else %}
        {{ site.title }}

## ds-training.md

      
              1 file
            
          
              23 forks
            
          
              11 comments
            
          
              117 stars
            
          
                hadley
                / ds-training.md
            
            
              Created
              March 13, 2015 18:49
            
              
                My advise on what you need to do to become a data scientist...
              
          
If you were to give recommendations to your "little brother/sister" on things
that they need to do to become a data scientist, what would those things be?

I think the "Data Science Venn Diagram" (http://drewconway.com/zia/2013/3/26/the-data-science-venn-diagram) is a great place to start. You need three things to be a good data scientist:

Statistical knowledge
Programming/hacking skills
Domain expertise

Statistical knowledge


## 2014-10-12_stop-working-directory-insanity.md

      
              1 file
            
          
              9 forks
            
          
              6 comments
            
          
              70 stars
            
          
                jennybc
                / 2014-10-12_stop-working-directory-insanity.md
            
            
              Last active
              September 23, 2022 04:43
            
              
                Stop the working directory insanity
              
          
    There are packages for this now!

2017-08-03: Since I wrote this in 2014, the universe, specifically Kirill Müller (https://github.com/krlmlr), has provided better solutions to this problem. I now recommend that you use one of these two packages:

rprojroot: This is the main package with functions to help you express paths in a way that will "just work" when developing interactively in an RStudio Project and when you render your file.
here: A lightweight wrapper around rprojroot that anticipates the most likely scenario: you want to write paths relative to the top-level directory, defined as an RStudio project or Git repo. TRY THIS FIRST.

I love these packages so much I wrote an ode to here.
I use these packages now instead of what I describe below. I'll leave this gist up for historical interest. 😆

  
## alg1-ropebwt2.txt
This document is a partial presentation of the RopeBWT2 pre-print

http://arxiv.org/abs/1406.0426

It is the transcript of a presentation made within the Medvedev group at Penn State
in July 2014. It focuses on illustrating some notions from the methods, and
illustrating and proving Algorithm 1. While this document does not cover the main
contribution of the RopeBWT2 paper, I hope it can be helpful towards understanding
the theoretical foundations that led to Algorithms 2 and 3.

## web-servers.md

      
              1 file
            
          
              931 forks
            
          
              236 comments
            
          
              5941 stars
            
          
                willurd
                / web-servers.md
            
            
              Last active
              April 23, 2024 23:07
            
              
                Big list of http static server one-liners
              
          
    Each of these commands will run an ad hoc http static server in your current (or specified) directory, available at http://localhost:8000. Use this power wisely.
Discussion on reddit.
Python 2.x

$ python -m SimpleHTTPServer 8000

  
## genbank_to_tbl.py
# requires biopython
# run like:
#   genbank_to_tbl.py "my organism name" "my strain ID" "ncbi project id" < my_sequence.gbk
#   writes seq.fsa, seq.tbl as output

import sys
from copy import copy
from Bio import SeqIO

def find_gene_entry(features, locus_tag):
	# Install Homebrew
	/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

	# Install QEMU OSX port with ARM support
	brew install qemu
	export QEMU=$(which qemu-system-arm)

	# Dowload kernel and export location
	brew install wget
	wget https://github.com/dhruvvyas90/qemu-rpi-kernel/raw/master/kernel-qemu-4.4.34-jessie
	# Install QEMU OSX port with ARM support
	sudo port install qemu +target_arm
	export QEMU=$(which qemu-system-arm)

	# Dowload kernel and export location
	curl -OL \
	https://github.com/dhruvvyas90/qemu-rpi-kernel/blob/master/kernel-qemu-4.1.7-jessie
	export RPI_KERNEL=./kernel-qemu-4.1.7-jessie

	# Download filesystem and export location
	#!/usr/bin/env gt

	function usage()
	io.stderr:write(string.format("Usage: %s <GFF annotation>\n" , arg[0]))
	os.exit(1)
	end

	if #arg < 1 then
	usage()
	end
	<!doctype html>
	<html lang="en">
	<head>
	<meta charset="utf-8">

	<title>
	{% if page.title %}
	{{ page.title }} \| {{ site.title }}
	{% else %}
	{{ site.title }}
	This document is a partial presentation of the RopeBWT2 pre-print

	http://arxiv.org/abs/1406.0426

	It is the transcript of a presentation made within the Medvedev group at Penn State
	in July 2014. It focuses on illustrating some notions from the methods, and
	illustrating and proving Algorithm 1. While this document does not cover the main
	contribution of the RopeBWT2 paper, I hope it can be helpful towards understanding
	the theoretical foundations that led to Algorithms 2 and 3.
	# requires biopython
	# run like:
	# genbank_to_tbl.py "my organism name" "my strain ID" "ncbi project id" < my_sequence.gbk
	# writes seq.fsa, seq.tbl as output

	import sys
	from copy import copy
	from Bio import SeqIO

	def find_gene_entry(features, locus_tag):