This library provides capabilities for querying Ensembl MySQL databases and for "administering" them. ensembldb3 is compatible with a range of Ensembl releases.
ensembldb3 began it's existence in 2009 as cogent.db.ensembl, a part of PyCogent. With the port of PyCogent to Python 3 (resulting in cogent3), it was decided to split the Ensembl querying code out into it's own project. This makes it easier to add new features and makes the project more visible to users.
ensembldb3 requires python 3.5+. Installation via pip into virtualenv's or conda environments (via pip) has been tested and is described below.
$ pip install git+http://github.com/cogent3/ensembldb3.git
The documentation can be viewed at readthedocs. You can build it yourself, but it requires sphinx and the read the docs Sphinx theme.
Install adds an admin script ensembldb3 which provides functions for downloading, installing and dropping databases. It uses rsync to download mysql dumps from the ensembl ftp site. ensembl_download based on a user provided config file indicating the release, species and their databases to download. (A sample config file is included for demonstration purposes.) The structure of the config file is:
[remote path] # required path=ftp.ensembl.org/ensembl/pub/ [local path] # required path=/tmp/ensembldb_download [release] # required release=85 [S.cerevisiae] db=core [Xenopus] db=core [Human] db=core,variation [compara] db=compara
| NOTE: | The species common name is used in the [] and the db's to be downloaded are comma separated. |
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You then download the corresponding databases as
$ ensembldb3 -c /path/to/your.cfg -v
The -v option means verbose. Use --help for more information.
If you are running this on a server, then we suggest using nohup to execute the command such that it doesn't die if, for instance, you close the laptop you use to login to the server... Doh! Here's an example
$ nohup ensembldb3 install -c download.cfg -m mysql.cfg -v > install.out 2>&1 & $ exit
When you log back in, the download progress will be in install.out.