AnyVar provides Python and REST interfaces to validate, normalize, generate identifiers, and register biological sequence variation according to the GA4GH Variation Representation Specification (VRS).
You are encouraged to browse issues. All known issues are listed there. Please report any issues you find.
Clone the repo and navigate to it:
git clone https://github.com/biocommons/anyvar
cd anyvarPoint ANYVAR_STORAGE_URI to an available PostgreSQL database:
export ANYVAR_STORAGE_URI=postgresql://anyvar:anyvar-pw@localhost:5432/anyvarSet SEQREPO_DATAPROXY_URI to local SeqRepo files:
export SEQREPO_DATAPROXY_URI=seqrepo+file:///usr/local/share/seqrepo/latestOr set SEQREPO_DATAPROXY_URI to a REST service instance:
export SEQREPO_DATAPROXY_URI=seqrepo+http://localhost:5000/seqrepoStart the AnyVar server:
uvicorn anyvar.restapi.main:app --reloadThis section is intended for developers who contribute to AnyVar.
- Python >= 3.9
- _Note: Python 3.11 is required for developers contributing to AnyVar
- Docker
git clone https://github.com/biocommons/anyvar.git
cd anyvar
make devready
source venv/3.11/bin/activate
pre-commit installFirst, you must install a local SeqRepo:
pip install seqrepo
export SEQREPO_VERSION=2024-02-20
sudo mkdir -p /usr/local/share/seqrepo
sudo chown $USER /usr/local/share/seqrepo
seqrepo pull -i $SEQREPO_VERSION
seqrepo update-latestNOTE: To check for the presence of newer snapshots, use the seqrepo list-remote-instances CLI command.
If you encounter a permission error similar to the one below:
PermissionError: [Error 13] Permission denied: '/usr/local/share/seqrepo/2024-02-20._fkuefgd' -> '/usr/local/share/seqrepo/2024-02-20'Try moving data manually with sudo:
sudo mv /usr/local/share/seqrepo/$SEQREPO_VERSION.* /usr/local/share/seqrepo/$SEQREPO_VERSIONWe recommend using Docker to install SeqRepo REST.
A Postgres or Snowflake database may be used with AnyVar. The Postgres database
may be either local or remote. Use the ANYVAR_STORAGE_URI environment variable
to define the database connection URL. AnyVar uses
SQLAlchemy 1.4 to provide database
connection management. The default database connection URL
is postgresql://postgres@localhost:5432/anyvar.
The database integrations can be modified using the following parameters:
ANYVAR_SQL_STORE_BATCH_LIMIT- in batch mode, limit VRS object upsert batches to this number; defaults to100,000ANYVAR_SQL_STORE_TABLE_NAME- the name of the table that stores VRS objects; defaults tovrs_objectsANYVAR_SQL_STORE_MAX_PENDING_BATCHES- the maximum number of pending batches to allow before blocking; defaults to50ANYVAR_SQL_STORE_FLUSH_ON_BATCHCTX_EXIT- whether or not flush all pending database writes when the batch manager exists; defaults toTrue
The Postgres and Snowflake database connectors utilize a background thread
to write VRS objects to the database when operating in batch mode (e.g. annotating
a VCF file). Queries and statistics query only against the already committed database
state. Therefore, queries issued immediately after a batch operation may not reflect
all pending changes if the ANYVAR_SQL_STORE_FLUSH_ON_BATCHCTX_EXIT parameter is sett
to False.
The following instructions are for using a docker-based Postgres instance.
First, run the commands in README-pg.md.
This will create and start a local Postgres docker instance. It will also create the
anyvar user with the appropriate permissions and create the anyvar database.
The Snowflake database and schema must exist prior to starting AnyVar. To point
AnyVar at Snowflake, specify a Snowflake URI in the ANYVAR_STORAGE_URI environment
variable. For example:
snowflake://sf_username:@sf_account_identifier/sf_db_name/sf_schema_name?password=sf_passwordSnowflake connection parameter reference
When running interactively and connecting to a Snowflake account that utilizes
federated authentication or SSO, add the parameter authenticator=externalbrowser.
Non-interactive execution in a federated authentication or SSO environment
requires a service account to connect. Connections using an encrypted or unencrypted
private key are also supported by specifying the parameter private_key=path/to/file.p8.
The key material may be URL-encoded and inlined in the connection URI,
for example: private_key=-----BEGIN+PRIVATE+KEY-----%0AMIIEvAIBA...
Environment variables that can be used to modify Snowflake database integration:
ANYVAR_SNOWFLAKE_STORE_PRIVATE_KEY_PASSPHRASE- the passphrase for an encrypted private keyANYVAR_SNOWFLAKE_BATCH_ADD_MODE- the SQL statement type to use when adding new VRS objects, one of:merge(default) - use a MERGE statement. This guarantees that duplicate VRS IDs will not be added, but also locks the VRS object table, limiting throughput.insert_notin- use INSERT INTO vrs_objects SELECT FROM tmp WHERE vrs_id NOT IN (...). This narrows the chance of duplicates and does not require a table lock.insert- use INSERT INTO. This maximizes throughput at the cost of not checking for duplicates at all.
If you choose to create the VRS objects table in advance, the minimal table specification is as follows:
CREATE TABLE ... (
vrs_id VARCHAR(500) COLLATE 'utf8',
vrs_object VARIANT
)Once the data dependencies are setup, start the REST server with:
uvicorn anyvar.restapi.main:appIn another terminal:
curl http://localhost:8000/infoTo run tests:
make testUse the environment variable ANYVAR_TEST_STORAGE_URI to specify the database to use
for tests, eg:
% export ANYVAR_TEST_STORAGE_URI=postgresql://postgres:postgres@localhost/anyvar_testCurrently, there is some interdependency between test modules -- namely, tests that rely
on reading data from storage assume that the data from test_variation has been
uploaded. A pytest hook ensures correct test order, but some test modules may not be
able to pass when run in isolation. By default, the tests will use a Postgres database
installation. To run the tests against a Snowflake database, change the
ANYVAR_TEST_STORAGE_URI to a Snowflake URI and run the tests.
AnyVar uses the Python Logging Module to
output information and diagnostics. By default, log output is directed to standard output
and the level is set to INFO. Alternatively, a YAML logging configuration may be specified
using the ANYVAR_LOGGING_CONFIG environment variable. The value must be the relative or
absolute path of a YAML file containing a valid logging configuration. The configuration
in this file will be loaded and used to configured the logging module.
For example:
version: 1
disable_existing_loggers: true
formatters:
standard:
format: "%(threadName)s %(asctime)s - %(name)s - %(levelname)s - %(message)s"
handlers:
console:
class: logging.StreamHandler
level: DEBUG
formatter: standard
stream: ext://sys.stdout
root:
level: INFO
handlers: [console]
propagate: yes
loggers:
anyvar.restapi.main:
level: INFO
handlers: [console]
propagate: no
anyvar.storage.sql_storage:
level: DEBUG
handlers: [console]
propagate: no