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.
QIIME wants this specific version, so let's compile and install it into the qiime/1.8.0 prefix.
Prepare Python source:
| #!/bin/bash | |
| #--- config | |
| SERVICE_NAME=galaxy | |
| RUN_AS=galaxy | |
| RUN_IN=/your/galaxy/directory | |
| #--- main actions |
| #!/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 |
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
| 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: |
| #!/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) |