antismash / downloader

antiSMASH web infrastructure NCBI download service

antiSMASH web infrastructure NCBI download service

A service to download sequences from NCBI for the antiSMASH web service.

Installation

Run the following (in a virtualenv):

git clone https://github.com/antismash/downloader
pip install downloader

Usage

All important runtime configuration is kept in a configuration file in TOML format.

Configuration Options

redis options

• url: URL to the redis database host
• port: Port the Redis database is listening on
• db: Database number of the Redis database

Example:

[redis]
url = redis_host
port = 6379
db = 0

antismash options

• queues: A list of queues to service. The input queue names are created by adding the download_suffix, see below.
• download_suffix: A suffix to append to an output queue name to get the download queue name.
• failed_queue: Queue to deposit failed jobs into.
• workdir: Path to directory holding all the antiSMASH job files.

Example:

[antismash]
queues = [ "jobs:fast", "jobs:queued", "jobs:development" ]
download_suffix = "downloads"
failed_queue = "jobs:failed"
workdir = "/path/to/antismash/upload/dir"

metrics options

• port: Port to expose Prometheus metrics on
• use_metrics: Turn metrics reporting on/off

Example:

[metrics]
port = 9151
use_metrics = true

License

All code is available under the Apache License version 2, see the LICENSE file for details.