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.. image:: https://readthedocs.org/projects/python-apollo/badge/?version=latest :target: http://python-apollo.readthedocs.io/en/latest/?badge=latest :alt: Documentation Status
Apollo is a Python library for interacting with
Apollo <https://github.com/gmod/apollo/>__. Arrow is its companion CLI tool.
`for the record <https://gitter.im/galaxy-genome-annotation/Lobby?at=5ebee6c049a1b7318479380d>`__ ... arrow makes working with Apollo SOOO much easier
— Nathan Dunn, Apollo Developer
.. code-block:: shell
pip install apollo
Example code to create a new organism and add yourself in the permission list:
.. code:: python
from apollo import ApolloInstance
wa = ApolloInstance('https://fqdn/apollo', 'jane.doe@fqdn.edu', 'password')
orgs = wa.organisms.add_organism(
"Yeast",
"/path/to/jbrowse/data",
genus='Saccharomyces',
species='cerevisiae',
public=False
)
# Give Apollo a second to process the uploaded organism.
time.sleep(1)
# Then add yourself to permission list
data = wa.users.update_organism_permissions(
"jane.doe@fqdn.edu",
"Yeast",
write=True,
export=True,
read=True,
)
If you have already created an Arrow config file (with command arrow init),
you can also get an ApolloInstance without writing credentials explicitely:
.. code:: python
from arrow.apollo import get_apollo_instance
wa = get_apollo_instance()
Or with the Arrow client:
.. code-block:: shell
$ arrow groups create_group university
{
"publicGroup": false,
"class": "org.bbop.apollo.UserGroup",
"name": "university",
"users": null,
"id": 558319
}
# THEN
$ arrow users get_users | \
jq '.[] | select(.username | contains("@tamu.edu")) | .username' | \
xargs -n1 arrow users add_to_group university
# OR
$ arrow users get_users | \
jq '.[] | select(.username | contains("@tamu.edu")) | .username' | \
paste -s -d',' | \
xargs arrow group update_membership 558319 --users
load_gff3 to more accurately load transcripts including the CDS as well as handle non-coding types more accurately.load_gff3 now uses the Apollo add_transcript method if it is a gene or mRNA typeFixed bug <https://github.com/galaxy-genome-annotation/python-apollo/issues/4>__ in deleteFeatures (Thanks @NeillGibson <https://github.com/NeillGibson>__)@abretaud <https://github.com/abretaud>__The content of docs and arrow directories is automatically generated from the code in the apollo directory. To regenerate it, install the latest version of the code, then run:
.. code-block:: shell
make rebuild
Available under the MIT License
This material is based upon work supported by the National Science Foundation under Grant Number (Award 1565146)
FAQs
Apollo API library
We found that apollo demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 3 open source maintainers collaborating on the project.
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