evolbioinfo/ngphylogeny repository overview

⁠NGPhylogeny.fr

A Django web application to make Phylogeny analysis.

⁠Installation

NGPhylogeny.fr requires python 2.7.

To install it:

• You may first install and activate a new conda environment:

conda create --name ngphylo python=2.7
source activate ngphylo

• Install all NGPhylogeny.fr dependencies:

pip install -r requirement.txt
apt-get install redis-server # Ubuntu / Debian

• Create Django databases

python manage.py makemigrations
python manage.py migrate
python manage.py createcachetable
python manage.py collectstatic

• Create admin user

python manage.py createsuperuser

• Load tool categories (flags)

python manage.py loaddata tool_flags

• Link NGPhylogeny.fr to a running Galaxy server

python manage.py creategalaxyserver --url=http://url_galaxy:port --activate
python manage.py addgalaxykey --user <superuser name> --galaxyurl http://url_galaxy:port --galaxykey <galaxy key>

• Import existing tools from Galaxy to NGPhylogeny.fr

python manage.py importtools --galaxyurl=http://url_galaxy:port \
                             --query="phylogeny" \
                             --flags=toolflags.txt \
                             --inputfields=toolfields.txt

• Two possibilities to link tools inputs and outputs

  1. Already computed links (preferable):

  python manage.py import_links --linkfile=toollinks.txt
  

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  1. Links computed on the fly (based on extension compatiblity, deprecated)

  python manage.py compute_tools_links --ignore=txt
  

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• Import Phylogeny workflows from the Galaxy Instance

It will import all workflows with name containing "oneclick" (case insensitive):

python manage.py importworkflows --galaxyurl=http://url_galaxy:port --wfnamefile=wfnames.txt

• Run Celery task queue

  1. Add following lines to NGPhylogeny_fr/settings/local.py:

  EMAIL_HOST = 'smtp.server.url'
  EMAIL_PORT = 587
  EMAIL_HOST_USER = 'smtp.user'
  EMAIL_HOST_PASSWORD = 'smtp.pass'
  EMAIL_USE_TLS=<True|False>
  

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  1. Start celery

  export PYTHONPATH=$PWD:$PYTHONPATH
  celery multi start 3 -l INFO -c:2 1 -c:3 1 -Q:1 default -Q:2 ncbi_blast -Q:3 monitor --app=NGPhylogeny_fr.celery:app
  celery beat --app=NGPhylogeny_fr.celery:app --loglevel=DEBUG --detach
  

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• Run the django server

python manage.py runserver

⁠Docker

You can run NGPhylogeny.fr via its docker image⁠:

⁠Using a remote galaxy instance:

Note: The remote galaxy instance must contain all necessary tools (listed here⁠).

docker run -p 8080:8000 evolbioinfo/ngphylogeny django_admin_username django_admin_password django_admin_email galaxy_url galaxy_api_key

⁠Using a custom local docker galaxy instance

We provide a galaxy docker image⁠ with all tools and workflows already installed (see this github repo⁠):

# Starting Docker image of Galaxy
docker run --privileged=true  \
           -p 8080:80 -p 8121:21 -p 8122:22 \
           evolbioinfo/ngphylogeny-galaxy
# MacOS => Starting NGPhylogeny.fr 
docker run -p 8000:8000 evolbioinfo/ngphylogeny admin admin@admin http://host.docker.internal:8080 admin
# Linux => Starting NGPhylogeny.fr
docker run -p 8000:8000 --net=host evolbioinfo/ngphylogeny admin admin@admin http://localhost:8080 admin

⁠Fully automatic with docker-compose⁠

The docker-compose.yml file in the docker folder is configured to set up a fully automatically running ngphylogeny instance, with 3 services:

1. A Galaxy server
2. A PostgreSQL database
3. The NGPhylogeny.fr server

First the file must be adapted to specific needs, by changing values between <> with real values, especially:

• NGPHYLO_HOST : The hostname or ip address of the server on which NGPhylogeny.fr will be running (for urls purpose)
• NGPHYLO_EMAIL_HOST: The smtp server for email notification
• NGPHYLO_EMAIL_PORT: The smtp port
• NGPHYLO_EMAIL_HOST_USER: The smtp user name
• NGPHYLO_EMAIL_HOST_PASSWORD: The smtp password
• NGPHYLO_EMAIL_USE_TLS: True or False, if smtp uses TLS
• NGPHYLO_DATABASE_NAME: Name of the PostgreSQL database (see below)
• NGPHYLO_DATABASE_USER: PostgreSQL user name (see below)
• NGPHYLO_DATABASE_PASSWORD: PostgreSQL password (see below)
• POSTGRES_USER: PostgreSQL user name (database name is the same)
• POSTGRES_PASSWORD: PostgreSQL password

Then to run the services:

> docker-compose up -d