mtholder’s gists

mtholder / complete-treemachine.sh

Created April 4, 2013 16:29

bash tab completion for the treemachine command

	_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 / gist:5587706

Created May 15, 2013 21:51

R function for a hacky approximation of the F_Tt factors in the Bryant et al SNAPP method as specialized for use by a homework assignment in the Kelly and Holder "Likelihood methods in Biology" class

	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 / gist:5587724

Created May 15, 2013 21:53

Python function for a hacky approximation of the F_Tt factors in the Bryant et al SNAPP method as specialized for use by a homework assignment in the Kelly and Holder "Likelihood methods in Biology" class

	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 / gist:5769321

Created June 12, 2013 21:33

test script for building opentree software on a "clean" machine

	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 / mb-and-beagle-from-svn.sh

Created December 4, 2013 02:42

compiling mrbayes with beagle in ubuntu. You may want to change the second line to whatever dir you would like to use as the parent of the prefix of the beagle installation.

	#!/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 / build-mb-3.2.2-with-beagle.sh

Created December 4, 2013 02:51

compile mb 3.2.2 with beagle on ubuntu

	#!/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 / grep_ot_code

Last active August 29, 2015 14:01

If you have checked the main open tree of life repos out into a directory which you lovingly call OPEN_TREE_REPO_ROOT in your env, then this will run grep on the files that appear to be java, python, or shell scripts in those repos.

	#!/bin/sh
	for repo in api.opentreeoflife.org deployed-systems gcmdr opentree ot-base oti ott peyotl phylografter taxomachine reference-taxonomy treemachine ;
	do
	for suffix in .java .py .sh
	do
	find "$OPEN_TREE_REPO_ROOT/$repo" -name "*$suffix" -exec grep -H $@ {} \; \| sed -e "s+$OPEN_TREE_REPO_ROOT/++"
	done
	done

mtholder / fetch_phylografter_study.py

Created May 31, 2014 02:11

(if you have peyotl installed and configured) this will download studies from phylografter and store each as NexSON in a file named <studyId>.json *WARNING*: this will overwrite <studyId>.json !

	#!/usr/bin/env python
	import sys
	from peyotl.api.phylografter import Phylografter
	pg = Phylografter()
	for study_id in sys.argv[1:]:
	pg.fetch_study(study_id, study_id + '.json')

mtholder / annotations.xsd

Last active August 29, 2015 14:02

hacky version of nexml/xsd/meta/annotations.xsd that allows any element inside a LiteralMeta

	<?xml version="1.0" encoding="UTF-8"?>
	<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" targetNamespace="http://www.nexml.org/2009"
	xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns="http://www.nexml.org/2009"
	xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:sawsdl="http://www.w3.org/ns/sawsdl"
	xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
	xmlns:xhtml="http://www.w3.org/1999/xhtml/datatypes/" elementFormDefault="qualified">

	<!-- <xs:annotation>
	<xs:documentation>
	This module defines annotations that can be attached to

mtholder / force_oti_reindexing_of_non_namespaced_ids.py

Created June 12, 2014 04:31

force_oti_reindexing_of_non_namespaced_ids.py

	#!/usr/bin/env python
	import sys
	from peyotl.api import APIWrapper
	aw = APIWrapper(phylesystem_api_kwargs={'get_from':'api'})
	pa = aw.phylesystem_api
	o = aw.oti
	for line in open(sys.argv[1], 'rU'):
	ls = line.strip()
	if '_' in ls:
	continue

Mark T. Holder mtholder