Install refgenie from GitHub releases or from PyPI with
pip install --user refgenie: install into user space.
pip install --user --upgrade refgenie: update in user space.
pip install refgenie: install into an active virtual environment.
pip install --upgrade refgenie: update in virtual environment.
See if your install worked by calling
refgenie -h on the command line. If the
refgenie executable in not in your
$PATH, append this to your
.bash_profile on macOS):
If you're using refgenie for the first time you'll need to initialize your genome folder and configuration file. Just select a folder where you want your genome assets to live, and then try:
refgenie init -c genome_folder/genome_config.yaml
refgenie commands all require knowing where this genome config file is. You can pass it on the command line all the time (using the
-c parameter), but this gets old. An alternative is to set up the
$REFGENIE environment variable like so:
Refgenie will automatically use the config file in this environmental variable if it exists. Add this to your
.profile if you want it to persist for future command-line sessions. You can always specify
-c if you want to override the value in the
$REFGENIE variable on an ad-hoc basis.
Now you can use the
refgenie list command to show local assets (which will be empty at first) or the
listr command to show available remote assets:
refgenie list refgenie listr
Populate some assets
Next you need to populate your genome folder with a few assets. You can either
pull existing assets or
build your own. Refgenie will manage them the same way. As an example, let's pull a bowtie2 index for a small genome, the human mitochondrial genome (it's called
rCRSd, the "Revised Cambridge Reference Sequence" on our server).
refgenie pull rCRSd/bowtie2_index
You can also read more about building refgenie assets.
refgenie seek command to get paths to local assets you have already built or pulled. For example, the one we just pulled:
refgenie seek rCRSd/bowtie2_index
Or, more generally:
refgenie seek GENOME/ASSET
That's it! Explore the HOW-TO guides in the navigation bar for further details about what you can do with these functions.
Managing server subscriptions
Refgenie populates the server list with http://refgenomes.databio.org by default. In case you want to
pull assets from other servers, which may serve a different set of assets, refgenie provides a command line access to the
genome_servers entry in the config file. Current list of server subscriptions is displayed by
refgenie list command.
Add new server
refgenie subscribe command to add an additional
refgenieserver instance to the config file:
refgenie subscribe -s http://another.refgenomes.server.org
This will append the provided argument to the current list of subscriptions. To start a new one, use
refgenie subscribe -s http://new.refgenomes.server.org -r
refgenie unsubscribe command to remove
refgenieserver instance from the config file:
refgenie unsubscribe -s http://refgenomes.databio.org