This is a pre-production deployment of Warehouse. Changes made here affect the production instance of PyPI (pypi.python.org).
Help us improve Python packaging - Donate today!
Project Description

A tool to manage complete (bacterial) genomes from the NCBI.

Most current release is 0.1.2.

Why?

GenomeBaser:
  1. Encourages best practice (uses rsync -> only update what’s needed)
  2. Despises filenames that aren’t easily understandable (symlinks to RefSeq based filename to Genus_species_strain.gbk)
  3. Give you what you will probably wan’t in the future (provides both .gbk and .fna. Generate PROKKA databases)
  4. Understands important differences (partitions complete chomosome and complete plasmind into separate buckets)

Installation

Something like:

$ pip install GenomeBaser

Alternatively:

$ wget https://github.com/mscook/GenomeBaser/archive/v0.1.2.tar.gz
$ tar -zxvf v0.1.2.tar.gz
$ cd v0.1.2
$ # May need sudo/root, BUT...
$ python setup.py install

Usage

Something like:

$ GenomeBaser --help
    Usage: GenomeBaser [OPTIONS] GENUS SPECIES OUT_DATABASE_LOCATION

    GenomeBaser is tool to manage complete (bacterial) genomes from the NCBI.

    Example usage:

          $ GenomeBaser.py Klebsiella pneumoniae ~/dbs

          $ # (wait a few months)...

          $ GenomeBaser Klebsiella pneumoniae ~/dbs

    By Mitchell Stanton-Cook (m.stantoncook@gmail.com)

    **More info at:** https://github.com/mscook/GenomeBaser

    Options:
      --check_deps / --no-check_deps  Check that non-python dependencies exist
      --help                          Show this message and exit.
Release History

Release History

0.1.2

This version

History Node

TODO: Figure out how to actually get changelog content.

Changelog content for this version goes here.

Donec et mollis dolor. Praesent et diam eget libero egestas mattis sit amet vitae augue. Nam tincidunt congue enim, ut porta lorem lacinia consectetur. Donec ut libero sed arcu vehicula ultricies a non tortor. Lorem ipsum dolor sit amet, consectetur adipiscing elit.

Show More

0.1.1

History Node

TODO: Figure out how to actually get changelog content.

Changelog content for this version goes here.

Donec et mollis dolor. Praesent et diam eget libero egestas mattis sit amet vitae augue. Nam tincidunt congue enim, ut porta lorem lacinia consectetur. Donec ut libero sed arcu vehicula ultricies a non tortor. Lorem ipsum dolor sit amet, consectetur adipiscing elit.

Show More

0.1.0

History Node

TODO: Figure out how to actually get changelog content.

Changelog content for this version goes here.

Donec et mollis dolor. Praesent et diam eget libero egestas mattis sit amet vitae augue. Nam tincidunt congue enim, ut porta lorem lacinia consectetur. Donec ut libero sed arcu vehicula ultricies a non tortor. Lorem ipsum dolor sit amet, consectetur adipiscing elit.

Show More

Download Files

Download Files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

File Name & Checksum SHA256 Checksum Help Version File Type Upload Date
GenomeBaser-0.1.2-py2-none-any.whl (106.4 kB) Copy SHA256 Checksum SHA256 py2 Wheel Sep 5, 2014
GenomeBaser-0.1.2.tar.gz (84.6 kB) Copy SHA256 Checksum SHA256 Source Sep 5, 2014

Supported By

WebFaction WebFaction Technical Writing Elastic Elastic Search Pingdom Pingdom Monitoring Dyn Dyn DNS Sentry Sentry Error Logging CloudAMQP CloudAMQP RabbitMQ Heroku Heroku PaaS Kabu Creative Kabu Creative UX & Design Fastly Fastly CDN DigiCert DigiCert EV Certificate Rackspace Rackspace Cloud Servers DreamHost DreamHost Log Hosting