def cli(ctx, paths, **kwds):
"""Install conda packages for tool requirements."""
conda_context = build_conda_context(ctx, **kwds)
if not conda_context.is_conda_installed():
auto_init = kwds.get("conda_auto_init", False)
failed = True
if auto_init:
if conda_context.can_install_conda():
if conda_util.install_conda(conda_context):
error("Attempted to install conda and failed.")
else:
failed = False
else:
error("Cannot install conda, failing conda_install.")
else:
error(
"Conda not configured - run planemo conda_init' or pass --conda_auto_init to continue."
)
if failed:
raise ExitCodeException(EXIT_CODE_FAILED_DEPENDENCIES)
return_codes = []
for conda_target in collect_conda_targets(ctx, paths):
ctx.log("Install conda target %s" % conda_target)
return_code = conda_util.install_conda_target(
conda_target, conda_context=conda_context)
return_codes.append(return_code)
return coalesce_return_codes(return_codes, assert_at_least_one=True)
def cli(ctx, paths, **kwds):
"""Install conda packages for tool requirements."""
conda_context = build_conda_context(ctx, **kwds)
if not conda_context.is_conda_installed():
auto_init = kwds.get("conda_auto_init", False)
failed = True
if auto_init:
if conda_context.can_install_conda():
if conda_util.install_conda(conda_context):
error("Attempted to install conda and failed.")
else:
failed = False
else:
error("Cannot install conda, failing conda_install.")
else:
error("Conda not configured - run planemo conda_init' or pass --conda_auto_init to continue.")
if failed:
raise ExitCodeException(EXIT_CODE_FAILED_DEPENDENCIES)
return_codes = []
for conda_target in collect_conda_targets(ctx, paths):
ctx.log("Install conda target %s" % conda_target)
return_code = conda_util.install_conda_target(
conda_target, conda_context=conda_context
)
return_codes.append(return_code)
return coalesce_return_codes(return_codes, assert_at_least_one=True)
def cli(ctx, **kwds):
"""Download and install conda.
This will download conda for managing dependencies for your platform
using the appropriate Miniconda installer.
By running this command, you are agreeing to the terms of the conda
license a 3-clause BSD 3 license. Please review full license at
http://docs.continuum.io/anaconda/eula.
Planemo will print a warning and terminate with an exit code of 7
if Conda is already installed.
"""
conda_context = build_conda_context(ctx, **kwds)
if conda_context.is_conda_installed():
warn(MESSAGE_ERROR_ALREADY_EXISTS % conda_context.conda_exec)
exit = EXIT_CODE_ALREADY_EXISTS
else:
exit = conda_util.install_conda(conda_context=conda_context, force_conda_build=True)
if exit:
warn(MESSAGE_ERROR_FAILED % conda_context.conda_exec)
else:
info(MESSAGE_INSTALL_OKAY % conda_context.conda_exec)
ctx.exit(exit)
def cli(ctx, **kwds):
"""Download and install conda.
This will download conda for managing dependencies for your platform
using the appropriate Miniconda installer.
By running this command, you are agreeing to the terms of the conda
license a 3-clause BSD 3 license. Please review full license at
http://docs.continuum.io/anaconda/eula.
Planemo will print a warning and terminate with an exit code of 7
if Conda is already installed.
"""
conda_context = build_conda_context(ctx, **kwds)
if conda_context.is_conda_installed():
warn(MESSAGE_ERROR_ALREADY_EXISTS % conda_context.conda_exec)
exit = EXIT_CODE_ALREADY_EXISTS
else:
exit = conda_util.install_conda(conda_context=conda_context,
force_conda_build=True)
if exit:
warn(MESSAGE_ERROR_FAILED % conda_context.conda_exec)
else:
info(MESSAGE_INSTALL_OKAY % conda_context.conda_exec)
ctx.exit(exit)
def cli(ctx, **kwds):
"""Download and install conda.
This will download conda for managing dependencies for your platform
using the appropriate Miniconda installer.
By running this command, you are agreeing to the terms of the conda
license a 3-clause BSD 3 license. Please review full license at
http://docs.continuum.io/anaconda/eula.
"""
conda_context = build_conda_context(**kwds)
return conda_util.install_conda(conda_context=conda_context)
def build_conda_context(ctx, **kwds):
"""Build a galaxy-lib CondaContext tailored to planemo use.
Using planemo's common command-line/global config options.
"""
condarc_override_default = os.path.join(ctx.workspace, "condarc")
conda_prefix = kwds.get("conda_prefix", None)
use_planemo_shell = kwds.get("use_planemo_shell_exec", True)
ensure_channels = kwds.get("conda_ensure_channels", "")
condarc_override = kwds.get("condarc", condarc_override_default)
use_local = kwds.get("conda_use_local", False)
shell_exec = shell if use_planemo_shell else None
conda_context = conda_util.CondaContext(conda_prefix=conda_prefix,
ensure_channels=ensure_channels,
condarc_override=condarc_override,
use_local=use_local,
shell_exec=shell_exec)
handle_auto_init = kwds.get("handle_auto_init", False)
if handle_auto_init and not conda_context.is_installed():
auto_init = kwds.get("conda_auto_init", True)
failed = True
if auto_init:
if conda_context.can_install_conda():
if conda_util.install_conda(conda_context):
error(MESSAGE_ERROR_FAILED_INSTALL)
else:
failed = False
else:
error(MESSAGE_ERROR_CANNOT_INSTALL)
else:
error(MESSAGE_ERROR_NOT_INSTALLING)
if failed:
raise ExitCodeException(EXIT_CODE_FAILED_DEPENDENCIES)
if handle_auto_init:
conda_context.ensure_conda_build_installed_if_needed()
return conda_context
def build_conda_context(ctx, **kwds):
"""Build a galaxy-lib CondaContext tailored to planemo use.
Using planemo's common command-line/globa config options.
"""
condarc_override_default = os.path.join(ctx.workspace, "condarc")
conda_prefix = kwds.get("conda_prefix", None)
use_planemo_shell = kwds.get("use_planemo_shell_exec", True)
ensure_channels = kwds.get("conda_ensure_channels", "")
condarc_override = kwds.get("condarc", condarc_override_default)
use_local = kwds.get("conda_use_local", False)
shell_exec = shell if use_planemo_shell else None
conda_context = conda_util.CondaContext(conda_prefix=conda_prefix,
ensure_channels=ensure_channels,
condarc_override=condarc_override,
use_local=use_local,
shell_exec=shell_exec)
handle_auto_init = kwds.get("handle_auto_init", False)
if handle_auto_init and not conda_context.is_installed():
auto_init = kwds.get("conda_auto_init", True)
failed = True
if auto_init:
if conda_context.can_install_conda():
if conda_util.install_conda(conda_context):
error(MESSAGE_ERROR_FAILED_INSTALL)
else:
failed = False
else:
error(MESSAGE_ERROR_CANNOT_INSTALL)
else:
error(MESSAGE_ERROR_NOT_INSTALLING)
if failed:
raise ExitCodeException(EXIT_CODE_FAILED_DEPENDENCIES)
if handle_auto_init:
conda_context.ensure_conda_build_installed_if_needed()
return conda_context