PipeTaxon exposes the ncbi taxonomy database as a REST API. It's intended to be consumed by bioinformatic pipelines or dataviz applications.
- Expose the entire taxonomy database as an API
- Provide a web interface for human interaction
- Optionally can query taxonomy from accession id
- Retrieve entire lineage from a taxonomy id
- LCA endpoint (retrieve the lowest common ancestor from a list of taxonomy id)
- Allow exclusion of ranks
http://pipetaxon.voorloopnul.com:8888
In a terminal copy and paste the following command:
curl https://raw.githubusercontent.com/voorloopnul/pipetaxon/master/install/install.sh | sudo bash
pipetaxon install
pipetaxon start
Go to your browser and type: http://localhost:8888
Pipetaxon is also a docker container, you should be able to get it up effortless by simply running the following commands:
docker pull voorloop/pipetaxon
docker run -p **80**:8000 voorloop/pipetaxon
if the default HTTP port is already in use or you don't have permission you can simply change it to any other port:
docker run -p **8888**:8000 voorloop/pipetaxon
Go to your browser and type:
http://localhost(when you choose port 80) orhttp://localhost:8888(or any other port you have chosen)
These instructions should be enough to get an instance of pipetaxon running in a ubuntu system. By default it have all ranks from NCBI and uses sqlite for database. Further instructions on how to setup pipetaxon with different databases and/or custom rank settings are available later in this document.
The following instructions are based on Ubuntu 18.04 other systems may have small differences in prerequisites and installation steps.
sudo apt-get install python3-venv
download the latest taxdump from ncbi
wget https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/new_taxdump/new_taxdump.tar.gz
decompress it
mkdir ~/data/ && tar -zxvf new_taxdump.tar.gz -C ~/data/
clone this repository
git clone https://github.com/voorloopnul/pipetaxon.git
enter project folder
cd pipetaxon
create a virtualenv
python3 -m venv ~/venv/pipetaxon
enter the virtualenv
source ~/venv/pipetaxon/bin/activate
install the requirements
pip install -r requirements.txt
run migrations
./manage.py migrate
build taxonomy database
./manage.py build_database --taxonomy ~/data/
build lineage
./manage.py build_database --lineage ~/data/
The --lineage command took 25 minutes and the --taxonomy 3 minutes in my I5 laptop
The accession data is quite large. If you need all the ids, SQLite might not be able to handle it very well.
We have tested nucl_gb.accession2taxid.gz with SQLite, the database size went to around 11GB and took one hour
to create all the 266 millions accession IDs from this file.
https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/nucl_gb.accession2taxid.gz
mkdir ~/data/ && tar -zxvf nucl_gb.accession2taxid.gz -C ~/data/
./manage.py build_database --accession ~/data/
SQLITE should suffice most use cases of standalone execution of pipetaxon, but if you need a full featured RDBMS like postgres or mysql your can easily configure it by changing the database config in settings.py to something like this:
DATABASES = {
'default': {
'ENGINE': 'django.db.backends.postgresql_psycopg2',
'HOST': 'localhost',
'NAME': 'pipetaxon',
'USER': '<username>',
'PASSWORD': '<password>',
}
}
By default all ranks present in NCBI will be part of your newly created taxonomy database, if you want to use a custom lineage
(removing ranks that don't add value to your project), you can easily do that by replacing the line VALID_RANKS = [] to something like:
VALID_RANKS = ["kingdom", "phylum", "class", "order", "family", "genus", "species"]
Keep in mind that you can't change this settings after building your database, if you already have one pipetaxon instance running, you first need to clear it's data
./manage.py build_database --clear ~/data/
Then you can run again the build process:
./manage.py build_database --taxonomy ~/data/
./manage.py build_database --lineage ~/data/
This project is licensed under the MIT License - see the LICENSE file for details
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