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josch / phenotips_tomcat_mysql.sh
Created August 28, 2018 11:10
Setting up phenotips on Ubuntu Xenial with Tomcat and MySQL
#!/bin/sh
set -exu
directory=ubuntu-xenial-robot
debootstrap --variant=minbase --include=dbus,systemd-sysv xenial "$directory" http://archive.ubuntu.com/ubuntu/
systemd-nspawn --boot --resolv-conf=copy-host --directory="$directory" &
pid=$!
@josch
josch / phenotips_tomcat.sh
Created August 28, 2018 11:09
Setting up phenotips on Ubuntu Xenial with Tomcat
#!/bin/sh
set -exu
directory=ubuntu-xenial-robot
debootstrap --variant=minbase --include=dbus,systemd-sysv xenial "$directory" http://archive.ubuntu.com/ubuntu/
systemd-nspawn --boot --resolv-conf=copy-host --directory="$directory" &
pid=$!
@josch
josch / gist:ba0617edc27018438d0a
Created July 2, 2015 16:46
#!/bin/sh
set -x
set -e
DEV=/dev/sdb
if ! sudo parted -lm 2>/dev/null | grep scsi | grep "$DEV" > /dev/null; then
echo "refusing to work on a device that is not a scsi disk" >&2
exit 1
@josch
josch / multibootiso.sh
Created March 7, 2014 14:04
create a disk image for a usb stick which combines all *.iso files found in the current directory into a multiboot image
#!/bin/sh
set -e
mkdir -p isomount
mkdir -p extmount
mkdir -p mainmount
cleanup() {
sudo umount isomount
@josch
josch / nfql_pygments.py
Created August 6, 2013 11:57
pygments lexer for nfql
class NFQLLexer(RegexLexer):
name = 'NFQL'
aliases = ['nfql']
filenames = ['*.flw']
tokens = {
'whitespace': [
(r'\n', Text),
(r'\s+', Text),
(r'\\\n', Text),
(r'#(\n|.*?\n)', Comment.Single),
@josch
josch / plnparse.py
Created June 5, 2013 13:59
attempt to parse deutsche bahn schedules in pln format
from urllib2 import Request, urlopen
from gzip import GzipFile
from cStringIO import StringIO
from zlib import decompress
from struct import unpack
from time import sleep
from datetime import timedelta, date, datetime
from lxml import etree
def get_id(station):
@josch
josch / pearson.py
Last active July 12, 2021 07:54
pearson hash and dolch word list experiments
from random import shuffle
from itertools import permutations
# dolch word list excluding "Santa Claus" (94 words)
words = [ "apple", "baby", "back", "ball", "bear", "bed", "bell", "bird",
"birthday", "boat", "box", "boy", "bread", "brother", "cake", "car",
"cat", "chair", "chicken", "children", "christmas", "coat", "corn",
"cow", "day", "dog", "doll", "door", "duck", "egg", "eye", "farm",
"farmer", "father", "feet", "fire", "fish", "floor", "flower",
"game", "garden", "girl", "good-bye", "grass", "ground", "hand",
@josch
josch / deltavision.py
Created June 5, 2013 13:33
reads a deltavision file and stores all images therein as png
#!/usr/bin/env python
#
# reads a deltavision file and stores all images therein as png
# this reader is fairly limited
#
# it expects a deltavision video in which there are two types of images, stored
# interleaved: ABABAB... Both types only have one channel. Each pair A and B is
# combined into an RGB image such that A is green and B is red
#
# example usage:
@josch
josch / pyrsegmentation.cpp
Created October 18, 2012 14:21
cvPyrSegmentation example
#include "opencv2/highgui/highgui.hpp"
#include "opencv2/core/core.hpp"
#include "opencv2/imgproc/imgproc.hpp"
#include "opencv2/imgproc/imgproc_c.h"
#include <iostream>
using namespace cv;
using namespace std;
@josch
josch / download.sh
Created October 12, 2012 19:09
download and satitize debian packages and sources files from snapshot.debian.org
#!/bin/sh
# this script first downloads and then sanitizes debian Packages and Sources
# files from snapshot.debian.org for every 5 days since the start of
# snapshot.debian.org
dist=sid
arch=i386
dates=`cat << END | python -c "import sys; exec sys.stdin.read()"
from datetime import date, timedelta as t
last = date.today()