def cli(ctx, path, **kwds):
"""Source output to activate a conda environment for this tool.
% . <(planemo conda_env bowtie2.xml)
% which bowtie2
TODO_PLACE_PATH_HERE
"""
conda_context = build_conda_context(use_planemo_shell_exec=False, **kwds)
conda_targets = collect_conda_targets(
path, conda_context=conda_context
)
installed_conda_targets = conda_util.filter_installed_targets(
conda_targets, conda_context=conda_context
)
env_name, exit_code = conda_util.build_isolated_environment(
installed_conda_targets, conda_context=conda_context
)
if exit_code:
error("Failed to build environmnt for request.")
return 1
ps1 = ps1_for_path(path, base="PRE_CONDA_PS1")
remove_env = "%s env remove -y --name '%s'" % (
conda_context.conda_exec, env_name
)
deactivate = conda_context.deactivate
activate = conda_context.activate
command = SOURCE_COMMAND % (
activate, env_name, ps1,
deactivate, remove_env
)
print(command)
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, path, **kwds):
"""Activate a conda environment for tool.
Source the output of this command to activate a conda environment for this
tool.
\b
$ . <(planemo conda_env seqtk_seq.xml)
Deactivate environment with conda_env_deactivate
(seqtk_seq_v6) $ which seqtk
/home/planemo/miniconda2/envs/jobdepsDkzcjjfecc6d406196737781ff4456ec60975c137e04884e4f4b05dc68192f7cec4656/bin/seqtk
(seqtk_seq_v6) $ conda_env_deactivate
$
"""
conda_context = build_conda_context(ctx,
use_planemo_shell_exec=False,
**kwds)
conda_targets = collect_conda_targets(ctx, [path])
installed_conda_targets = conda_util.filter_installed_targets(
conda_targets, conda_context=conda_context)
env_name, exit_code = conda_util.build_isolated_environment(
installed_conda_targets, conda_context=conda_context, quiet=True)
if exit_code:
error("Failed to build environment for request.")
return 1
ps1 = ps1_for_path(path, base="PRE_CONDA_PS1")
remove_env = "%s env remove -y --name '%s'" % (conda_context.conda_exec,
env_name)
deactivate = conda_context.deactivate
activate = conda_context.activate
command = SOURCE_COMMAND % (activate, env_name, ps1, deactivate,
remove_env)
print(command)
def cli(ctx, path, **kwds):
"""Install conda packages for tool requirements."""
conda_context = build_conda_context(**kwds)
return_codes = []
for conda_target in collect_conda_targets(path):
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, handle_auto_init=True, **kwds)
return_codes = []
for conda_target in collect_conda_targets(ctx, paths, recursive=kwds["recursive"]):
ctx.log("Install conda target %s" % conda_target)
return_code = conda_util.install_conda_target(
conda_target, conda_context=conda_context, skip_environment=kwds.get("global", False)
)
return_codes.append(return_code)
return coalesce_return_codes(return_codes, assert_at_least_one=True)
def cli(ctx, path, **kwds):
"""Install conda packages for tool requirements."""
conda_context = build_conda_context(**kwds)
return_codes = []
for conda_target in collect_conda_targets(path):
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, handle_auto_init=True, **kwds)
return_codes = []
for conda_target in collect_conda_targets(ctx,
paths,
recursive=kwds["recursive"]):
ctx.log("Install conda target %s" % conda_target)
return_code = conda_util.install_conda_target(
conda_target,
conda_context=conda_context,
skip_environment=kwds.get("global", False))
return_codes.append(return_code)
return coalesce_return_codes(return_codes, assert_at_least_one=True)
def cli(ctx, path, **kwds):
"""Activate a conda environment for tool.
Source the output of this command to activate a conda environment for this
tool.
\b
$ . <(planemo conda_env seqtk_seq.xml)
Deactivate environment with conda_env_deactivate
(seqtk_seq_v6) $ which seqtk
/home/planemo/miniconda2/envs/jobdepsDkzcjjfecc6d406196737781ff4456ec60975c137e04884e4f4b05dc68192f7cec4656/bin/seqtk
(seqtk_seq_v6) $ conda_env_deactivate
$
"""
conda_context = build_conda_context(ctx, use_planemo_shell_exec=False, **kwds)
conda_targets = collect_conda_targets(
ctx, [path], conda_context=conda_context
)
installed_conda_targets = conda_util.filter_installed_targets(
conda_targets, conda_context=conda_context
)
env_name, exit_code = conda_util.build_isolated_environment(
installed_conda_targets, conda_context=conda_context, quiet=True
)
if exit_code:
error("Failed to build environmnt for request.")
return 1
ps1 = ps1_for_path(path, base="PRE_CONDA_PS1")
remove_env = "%s env remove -y --name '%s'" % (
conda_context.conda_exec, env_name
)
deactivate = conda_context.deactivate
activate = conda_context.activate
command = SOURCE_COMMAND % (
activate, env_name, ps1,
deactivate, remove_env
)
print(command)
