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ziemertlab/arts

By ziemertlab

•Updated almost 3 years ago

Antibiotic Resistant Target Seeker (arts.ziemertlab.com)

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ziemertlab/arts repository overview

Note: This repository was last updated in 2017!

Antibiotic Resistant Target Seeker (ARTS) is a webserver and analysis pipeline for screening for known and putative antibiotic resistance markers in order to identify and prioritize their corresponding biosynthetic gene clusters.

⁠I. Arts webserver setup on Linux (tested Debian 8 Jesse)

A. Install and Quickstart

#Update and install dependencies if not present
(1) sudo apt-get update
(2) sudo apt-get install git python-dev python-pip liblzma-dev libxml2-dev libxslt-dev zlib1g-dev virtualenv libxext-dev python-qt4 qt4-dev-tools apt-transport-https redis-server
#Tree drawing: If no Xserver is present install xdm or use lightweight xvfb as alternative.
(2.1a) sudo apt-get install  xserver-xorg xdm  xfonts-base xfonts-100dpi xfonts-75dpi
(2.1b) sudo apt-get install xvfb

#Clone ARTS git repository and begin install (change to desired directory, ex: cd ~)
(3) git clone https://bitbucket.org/ziemertlab/arts
(4) cd arts
#setup virtual environment (optional but recommended, ex: stored in current arts folder)
(4.1) virtualenv --system-site-packages .env
(4.2) source .env/bin/activate

# use sudo if installing without virtualenv
(5) pip install -I -r requirements.txt

# Setup working directories and configuration
# config file can be stored anywhere and referenced by environment variable: ARTS_SETTINGS
# If ARTS_SETTINGS is not set arts looks for defaults in this order: 
# ..webapp/config/activeconfig.conf, /etc/artsapp.conf, ..webapp/config/artsapp_default.conf
# Remember to remove "#" if you wish to change a setting

(6) cp webapp/app/config/artsapp_default.conf webapp/app/config/activeconfig.conf

# Edit config using desired editor. Secret key can be generated via this command: python -c 'import os;print repr(os.urandom(24))'
(7) nano webapp/app/config/activeconfig.conf

#QUICKSTART: Runs a simple development server
(8) redis-server --daemonize yes
(9) python webapp/runwebapp.py

### DONE. Web app should be visible in browser at http://localhost:5000 (http://127.0.0.1:5000)
### Jobs will not run until runjobs.py daemon is setup. Use 'redis-cli shutdown' to shutdown redis job queue server

B. Webserver setup using nginx and uwsgi - Faster and better multi-user support

### continued from step (6) cmds run from arts git directory

(7) sudo apt-get install nginx libpcre3 libpcre3-dev; pip install uwsgi

# Example using default http tcp (logs stored in /tmp/)
# assuming only sites-enabled are 'default' from nginx install
# if other sites present rename server_name
(8) sudo cp webapp/config/nginx.conf /etc/nginx/sites-available/artswebapp
(9) sudo ln -s ../sites-available/artswebapp /etc/nginx/sites-enabled/artswebapp && sudo rm /etc/nginx/sites-enabled/default
(10) sudo service nginx restart
(11) redis-server --daemonize yes
(12) uwsgi --ini webap/config/uwsgi.conf
⁠II. Arts analysis daemon runjobs.py setup A. Antismash install prereqs long-orfs extract build-icm glimmer3

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almost 3 years ago

docker pull ziemertlab/arts