brantfaircloth

def fib(n):    # write Fibonacci series up to n
    a, b = 0, 1
    while b < n:
        print b,
        a, b = b, a+b

brantfaircloth

#!/usr/bin/env python

import sys
from numpy import random

print random.random_integers(1,1000000000,int(sys.argv[1]))

brantfaircloth

source /usr/local/antigen/antigen.zsh
# Load the oh-my-zsh's library.
antigen use oh-my-zsh

# Bundles from the default repo (robbyrussell's oh-my-zsh).
antigen bundle command-not-found

# Syntax highlighting bundle.
antigen bundle zsh-users/zsh-syntax-highlighting

brantfaircloth

#!/usr/bin/env zsh
 
# assumes we're using coreutils on osx.  if GNU/linux, then 
# replace gwc with wc and gsed with sed

for i in ExaBayes_parameters.*.{0-3}$;
do
    echo "working on ${i}"
    lineno=`gwc -l < $i`;line=`tail -n -1 $i`;gsed -e "${lineno}i ${line}" $i:r.continued1."${i##*.}" > $i:r.continued1.mod."${i##*.}";
done

brantfaircloth

• create shell script to run configuration of job. Save the following as configure.sh:

  #!/bin/bash
  export LD_LIBRARY_PATH=/usr/local/boost/1.44.0/gcc447/lib:${LD_LIBRARY_PATH}
  
  cd /escratch4/tcg_tech2/tcg_tech2_Mar_03/test-ACN5P
  
  # create a basecalls directory to hold our output
  

/usr/local/bcl2fastq/1.8.4/bin/configureBclToFastq.pl \

brantfaircloth

#!/usr/bin/env python
# -*- coding: utf-8 -*-

"""
(c) 2015 Brant Faircloth || http://faircloth-lab.org/
All rights reserved.

This code is distributed under a 3-clause BSD license. Please see
LICENSE.txt for more information.

brantfaircloth

Stacks on Ubuntu 14.04 LTS

• install dependencies:

    apt-get install build-essential zlib1g-dev vim
    apt-get install libsparsehash-dev mysql-server php5 apache2 php-mdb2 php-mdb2-driver-mysql libdbd-mysql-perl samtools libbam-dev
  

• for ease of compilation, symlink sparsehash to /usr/local/include:

sudo ln -s /usr/include/google /usr/local/include/sparsehash

brantfaircloth

#!/usr/bin/env python
# -*- coding: utf-8 -*-

"""
(c) 2014 Brant Faircloth || http://faircloth-lab.org/
All rights reserved.

This code is distributed under a 3-clause BSD license. Please see
LICENSE.txt for more information.

brantfaircloth

#!/usr/bin/env python
# -*- coding: utf-8 -*-

"""
(c) 2014 Brant Faircloth || http://faircloth-lab.org/
All rights reserved.

This code is distributed under a 3-clause BSD license. Please see
LICENSE.txt for more information.

brantfaircloth

#!/usr/bin/env python
# -*- coding: utf-8 -*-

from random import shuffle

# create a list of all labels - NOTE that i've used 2 here because we have
# 2 individuals in pop A and 2 in pop B
label_list = ["population-A"] * 2 + ["population-B"] * 2
# do something 100 times
for i in xrange(100):