Marcus Breese mbreese

Environmental Modules

Environment Modules is a utility that has been used to manage executables and paths for high-performance computing clusters for multiple decades (1991!). The basic idea is that you can use modules to adapt your processing environment (and $PATH) to make sure that your environment is consistent. Importantly, this allows system administrators the ability to install and maintain multiple versions of software for different users. This tool can also be used to effectively manage your bioinformatics processing pipelines to ensure consistent analysis runs. For example, if you have a set of samples that will need to be analyzed consistently over a long time span, you could use modules to make sure that the same version of a program is used throughout the entire experiment while letting you use newer versions for different experiments.

Installation

If you are running your samples on a computing cluster, chances are you are already using modules to configure your environment (add progra

	#!/usr/bin/env python

	import sys

	prefix="VEP_"
	vep_info_name = "CSQ"


	def parse_info_format(line):
	###INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Allele\|Consequence\|IMPACT\|SYMBOL\|Gene\|Feature_type\|...">

	#!/bin/bash
	TARGETDIR=$1
	if [ "$TARGETDIR" = "" ]; then
	TARGETDIR=$(python -c 'import os; print os.path.realpath("local")')
	fi
	mkdir -p $TARGETDIR

	libevent() {
	curl -LO https://github.com/libevent/libevent/releases/download/release-2.0.22-stable/libevent-2.0.22-stable.tar.gz
	tar -zxvf libevent-2.0.22-stable.tar.gz

	docker run -v /Users/mbreese/tmp:/tmp1 -w /tmp1 -i centos:7 /bin/bash -s <<EOF
	date > foo
	echo 'foo' >> foo
	cat /etc/redhat-release >> foo
	whoami >> foo
	EOF

	production:
	disable_default: true
	methods:
	- adapter: Gitorious::Authentication::LDAPAuthentication
	server: 10.1.?.?
	port: 389
	base_dn: DC=domain,DC=org
	# bind_username: binduser
	# bind_password: binduserpass
	user_filter:

	CREATE ROLE db_user LOGIN ENCRYPTED PASSWORD 'secret-password' NOSUPERUSER INHERIT NOCREATEDB NOCREATEROLE NOREPLICATION;
	CREATE DATABASE db_name WITH OWNER db_user;
	GRANT ALL PRIVILEGES ON DATABASE db_name TO db_user;