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Ensembl's VEP (Variant Effect Predictor) is popular for how it picks a single effect per gene as detailed here, its CLIA-compliant HGVS variant format, and Sequence Ontology nomenclature for variant effects.

To follow these instructions, we'll assume you have these packaged essentials installed:

## For Debian/Ubuntu system admins ##
sudo apt-get install -y build-essential git libncurses-dev

## For RHEL/CentOS system admins ##
sudo yum groupinstall -y 'Development Tools'
sudo yum install -y git ncurses-devel

QIIME 1.8.0 on CentOS 6.5

Installing QIIME manually in it's own prefix on CentOS 6.5. Our cluster has a network-mounted applications directory, so I wanted to install it once there, so all cluster nodes could use it.

Reference: http://qiime.org/install/install.html

Python 2.7.3

QIIME wants this specific version, so let's compile and install it into the qiime/1.8.0 prefix.

Prepare Python source:

	#!/usr/bin/env python3

	import requests
	import hashlib
	import getpass

	password = getpass.getpass()
	hash = hashlib.sha1(password.encode("utf8")).hexdigest().upper()
	head, rest = hash[:5], hash[5:]
	r = requests.get("https://api.pwnedpasswords.com/range/%s" % head)

	Download Google Drive files with WGET

	Example Google Drive download link:

	https://docs.google.com/open?id=[ID]
	To download the file with WGET you need to use this link:

	https://googledrive.com/host/[ID]

	Example WGET command:

	#!/bin/bash

	NAME="hello_app" # Name of the application
	DJANGODIR=/webapps/hello_django/hello # Django project directory
	SOCKFILE=/webapps/hello_django/run/gunicorn.sock # we will communicte using this unix socket
	USER=hello # the user to run as
	GROUP=webapps # the group to run as
	NUM_WORKERS=3 # how many worker processes should Gunicorn spawn
	DJANGO_SETTINGS_MODULE=hello.settings # which settings file should Django use
	DJANGO_WSGI_MODULE=hello.wsgi # WSGI module name

	#!/bin/bash

	#--- config

	SERVICE_NAME=galaxy
	RUN_AS=galaxy
	RUN_IN=/your/galaxy/directory

	#--- main actions