def plugin(command, name):
"""
Enable or disable plugins
genomepy plugin list show plugins and status
genomepy plugin enable [NAME(S)] enable plugins
genomepy plugin disable [NAME(S)] disable plugins
"""
genomepy.manage_plugins(command, name)
# redirect all messages to a logfile
with open(logfile, "w") as log:
with contextlib.redirect_stdout(log), contextlib.redirect_stderr(log):
genomepy.logger.remove()
genomepy.logger.add(
logfile,
format=
"<green>{time:HH:mm:ss}</green> <bold>|</bold> <blue>{level}</blue> <bold>|</bold> {message}",
level="INFO",
)
# list user plugins
active_plugins = genomepy.config.config.get("plugin", [])
if active_plugins:
print("Deactivating user plugins")
genomepy.manage_plugins("disable", active_plugins)
# select user specified provider
if provider is None:
# select a provider with the annotation
provider = providers[assembly]["annotation"]
try:
genomepy.install_genome(
name=assembly,
provider=provider,
genomes_dir=genomes_dir,
only_annotation=True,
force=True,
)