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, 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, brew=None, skip_install=False, shell=None):
"""List commands to inject brew dependencies.
Display commands used to modify environment to inject tool's brew
dependencies.
\b
% . <(planemo brew_env bowtie2.xml)
% which bowtie2
/home/john/.linuxbrew/Cellar/bowtie2/2.1.0/bin/bowtie2
By default this will attempt to attempt to install these recipes as needed.
This automatic installation can be skipped with the ``--skip_install``
flag.
Intead of injecting the enviornment into your current shell using the above
idiom, the ``--shell`` flag can be sent to launch a new subshell when
sourced.
\b
% . <(planemo brew_env --skip_install --shell bowtie2.xml)
(bowtie2) % which bowtie2
/home/john/.linuxbrew/Cellar/bowtie2/2.1.0/bin/bowtie2
"""
tool_xml = load_tool(path)
mock_args = bunch.Bunch(brew=brew)
brew_context = brew_exts.BrewContext(mock_args)
requirements, containers = parse_requirements_from_xml(tool_xml)
lines = []
for recipe_context in brew_util.requirements_to_recipe_contexts(
requirements,
brew_context
):
if not skip_install:
brew_exts.versioned_install(recipe_context)
lines = brew_exts.build_env_statements_from_recipe_context(
recipe_context
)
split_lines = lines.split("\n")
lines.extend(split_lines)
if shell:
# TODO: Would be cool if this wasn't a bunch of random hackery.
launch_shell = os.environ.get("SHELL")
if "bash" in launch_shell:
ps1 = ps1_for_path(path)
launch_shell = '(source ~/.bashrc; env PS1="%s" %s --norc)' % (
ps1,
launch_shell,
)
lines.extend([launch_shell])
print(";".join(lines))
else:
print("\n".join(lines))
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)