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lbeltrame / nonworking.yaml
Created Dec 22, 2014
Non working config file
View nonworking.yaml
- algorithm:
aligner: bwa
archive: cram
clinical_reporting: true
coverage: my_regions
coverage_depth: high
coverage_interval: regional
effects: vep
indelcaller: scalpel

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lbeltrame / gogs.init
Last active Apr 16, 2016
CentOS Gogs init script
View gogs.init
# /etc/rc.d/init.d/gogs
# Runs the Gogs Go Git Service.
# chkconfig: - 85 15
lbeltrame / gist:9888910
Created Mar 31, 2014
Calculate coverage for a directory containing BAM files, given a BED file
View gist:9888910
# This file is part of utils
# Copyright (C) 2014 Luca Beltrame <>
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Library General Public
# License as published by the Free Software Foundation; either
# version 2 of the License, or (at your option) any later version.
#!/usr/bin/env python
# encoding: utf-8
import json
import os
import subprocess
import sys
import requests
from argparse import ArgumentParser
lbeltrame /
Last active Dec 11, 2015
PyQt4 + PyKDE4 script to auto-create IPython notebooks based on date, including starting the interpreter and browser (chromium). Depends upon having a "nbserver" profile set up in IPython. Depends upon: pathlib, psutil, PyQt4, PyKDE4, Pynotify.
#!/usr/bin/env python
from datetime import datetime
import sys
from IPython.nbformat import current
from pathlib import Path
from PyKDE4.kdecore import KStandardDirs
from PyKDE4.kio import KRun
import PyQt4.QtCore as QtCore
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