Joshua Gourneau gourneau

🎯

Focusing

Hacker on planet earth

gourneau / launch.sh

Created January 11, 2013 00:21

Plugin to create PDF at the end of a run for Ion Torrent

	#!/bin/bash

	VERSION="0.1"

	#Set the URL for the API requests
	plugin_url=http://127.0.0.1/rundb/api/v1/results/${RUNINFO__PK}/plugin/
	page_url=http://127.0.0.1/${RUNINFO__URL_ROOT}/

	#Set the HTTP Headers
	api_header="Content-Type: application/json;Accept: application/json"

gourneau / plugin_hunt.py

Created February 1, 2013 21:55

	from __future__ import division
	import requests
	import math
	import sys

	def human_size(size_bytes):
	"""
	format a size in bytes into a 'human' file size, e.g. bytes, KB, MB, GB, TB, PB
	Note that bytes/KB will be reported in whole numbers but MB and above will have greater precision
	e.g. 1 byte, 43 bytes, 443 KB, 4.3 MB, 4.43 GB, etc

gourneau / gist:5001310

Created February 21, 2013 01:54

	{ "pluginconfig" :
	{
	"torrent_variant_caller":{
	"downsample_to_coverage":2000,
	"min_indel_count_for_genotyping":5,
	"min_mapping_quality_score":4,
	"min_allele_frequency":0.2,
	"hp_low_stringency":0,
	"hp_min_cov_each_strand":3,
	"hp_stb_fpe_min_coverage":30,

gourneau / planet.py

Created February 25, 2013 20:23

	import random

	class shorter_float(float):
	"""A float which returns only 3 digits after the decimal"""
	def __repr__(self):
	return "%0.3f" % self

	ires = 100.0 # Inverse resolution
	left = -100
	right = 101

gourneau / instance.html

Created March 7, 2013 00:57

	<!DOCTYPE html>
	<html lang="en">
	<head>
	<link rel="stylesheet" media="all" href="/site_media/resources/bootstrap/css/bootstrap.min.css" type="text/css">
	<script type="text/javascript" src="/site_media/resources/jquery/jquery-1.8.2.js"></script>
	<script type="text/javascript" src="/site_media/resources/bootstrap/js/bootstrap.min.js"></script>

gourneau / gist:5249514

Created March 26, 2013 21:34

	blackbird.ite

	```apace
	##
	## Server-Pool Size Regulation (MPM specific)
	##

	# prefork MPM
	# StartServers: number of server processes to start
	# MinSpareServers: minimum number of server processes which are kept spare

gourneau / pl.py

Created April 5, 2013 00:15

	from __future__ import division
	import requests
	import math

	r = requests.get("http://ionwest.itw/rundb/api/v1/pluginresult/?format=json&endtime__gte=2013-01-10&limit=0")

	s = [o["state"] for o in r.json["objects"] if o["state"] != "Queued" or o["state"] != "Pending"]

	success = 0
	error = 0

gourneau / pg_activity.sh

Created April 16, 2013 23:16

Install pg_activity on Ubuntu 10.04 from source

	#https://github.com/julmon/pg_activity

	#install
	sudo aptitude install postgresql-server-dev-8.4 python-virtualenv
	virtualenv --no-site-packages venv
	source venv/bin/activate
	sudo chmod -R 777 /usr/share/man/man1/
	pip install https://github.com/julmon/pg_activity/archive/master.zip

	#run

gourneau / startplugin.py

Created May 29, 2013 19:56

Start Ion Torrent plugins via the API using a Python script

	import requests
	import json

	#load config from your json files, and convert it to a python dict
	config = {}
	payload = {'plugin': ["HelloWorld"], "pluginconfig" : config }
	headers = {'content-type': 'application/json'}

	#the number is the primary key of the result to run the plugin on
	r = requests.post("http://bebop.itw/rundb/api/v1/results/224/plugin/", data=json.dumps(payload), auth=('ionadmin', 'ionadmin'),headers=headers)

gourneau / email.scpt

Created July 8, 2013 05:29

AppleScript script to compose email using Microsoft Outlook

	tell (current date) to get (it's month as integer) & "-" & day & "-" & (it's year as integer)
	set MyDay to the result as text
	set Mytitle to "Daily Email - " as text
	set Mytitle to Mytitle & MyDay

	tell application "Microsoft Outlook"

	set newMessage to make new outgoing message with properties {subject:Mytitle}
	make new recipient at newMessage with properties {email address:{name:"Name", address:"test@example.com"}}
	#make new cc recipient at newMessage with properties {email address:{name:"Name", address:"test@example.com"}}