mtholder

#!/bin/sh
PREFIX_PARENT="${HOME}/envs"
set -x


mkdir -p "${PREFIX_PARENT}/beagle" || exit
svn checkout https://beagle-lib.googlecode.com/svn/trunk/ beagle-lib  || exit
cd beagle-lib
sh autogen.sh 
mkdir build  || exit

mtholder

sudo apt-get install git
git clone git://github.com/mtholder/ot-vagrant.git
cd ot-vagrant/
git pull origin 
cat >web2py_passwords.sh <<ENDOFHEREDOC
#!/bin/sh
export WEB2PY_DB_USER=greatusernamehere
export WEB2PY_DB_PASSWD=somepassword

ENDOFHEREDOC

mtholder

def calc_F_Tt(r_Tb, n_Tt, r_Tt, param_vec):
    if r_Tt > n_Tt:
        return 0.0
    Ne = param_vec[ParamOrder.PopSize].value
    mu = param_vec[ParamOrder.MutRate].value
    tau = param_vec[ParamOrder.DivTime].value

    # The probability of coalescence along the Turkish branch goes to 1 as tau gets big or Ne gets small
    prob_coalescence = 1 - exp(-tau/(2.0*Ne))
    prob_no_coalescence = 1 - prob_coalescence

mtholder

calc.F_Tt <- function (r_Tb, n_Tt, r_Tt, param.vec) {
    if (r_Tt > n_Tt) {
        return (0.0);
    }
    # unnumbered eqn on the bottom of page 5
    Ne <- param.vec[2];
    mu <- param.vec[3];
    tau <- param.vec[4];

    # The probability of coalescence along the Turkish branch goes to 1 as tau gets big or Ne gets small

mtholder

_treemachine()
{
    local cur=${COMP_WORDS[COMP_CWORD]}
    local prev=${COMP_WORDS[COMP_CWORD-1]}
    if test $prev = "treemachine"
    then
        # if the previous word was treemachine, prompt with the commands
        COMPREPLY=( $(compgen -W "addtree reprocess deletetrees jsgol fulltree fulltree_sources fulltreelist mrpdump graphml csvdump justtrees sourceexplorer listsources biparts mapsupport getlicanames counttips diversity labeltips getupdatedlist" -- $cur))
    else
        #otherwise do file completion.  Which seems tougher than it should be...

mtholder

//	Copyright (C) 2012 Mark T. Holder
//
//	Based on example/splitsinfile/splitsinfile.cpp in NEXUS class library
//
//	After NCL has been installed at ${NCL_PREFIX}
//
//		g++ newick2taxalist.cpp -o newick2taxalist -I "${NCL_PREFIX}/include" -lncl -L "${NCL_PREFIX}/lib/ncl"
//
//	Takes a newick file and prints out the taxa labels, one per line.
//

mtholder

#!/bin/sh
# Script to use NCLconverter to convert TreeBase NEXUS files to newick
# Invocation:
#   sh range_of_treebase2newick.sh 10000 10100
# in a directory with filenames like S10001.nex to convert each file
# name like S10000.nex up to file S10100.nex to newick.
# you should get files like:
#   outS####.tre  newick tree for the first trees block
#   2outS####.tre , 3outS####.tre , etc if the file has multiple output blocks
#   outS####.NameTranslationFile.txt is an ad hoc xml description of the name mapping

mtholder

#!/usr/bin/env python
'''
Example of a client of the demo of the TNRS API described at:
    http://www.evoio.org/wiki/Phylotastic/TNRS

Reads names (separated by newline characters) from file names passed in as
    command-line arguments (or reads name from standard input if no arguments
    are given).

Outputs tab-delimited summary of the matches for each query sorted by score of 

mtholder

#!/bin/sh
# You might want to modify the first line to specify your own install location.
#    In theory the rest should not need tweaking...
export GCC_PREFIX="$HOME/gcc4.7"

# Hopefully, you can tweak these as they get out of date, but the download URL's
#      may not be stable to text substitution.
GMP_DOWNLOAD_VERSION=gmp-5.0.5
MPFR_DOWNLOAD_VERSION=mpfr-3.1.0
MPC_DOWNLOAD_VERSION=mpc-0.8.2

mtholder

#!/usr/bin/env python
import sys, math
v_list = [float(value) for value in sys.stdin]
offset = max(v_list)
n = len(v_list)
sum_exps = sum([math.exp(v - offset) for v in v_list])
mean_exps = sum_exps/n
sys.stdout.write('Log of mean of the exp of %d values is:\n' %  n)
sys.stdout.write('%8.7f\n' % (math.log(mean_exps) + offset))