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, brew=None):
"""Install tool requirements using brew. (**Experimental**)
An experimental approach to versioning brew recipes will be used.
See full discussion on the homebrew-science issues page here -
https://github.com/Homebrew/homebrew-science/issues/1191. Information
on the implementation can be found at
https://github.com/jmchilton/platform-brew
until a more permanent project home is setup.
"""
for (tool_path, tool_xml) in load_tool_elements_from_path(path):
ctx.log('Brewing requirements from tool %s',
click.format_filename(tool_path))
mock_args = bunch.Bunch(brew=brew)
brew_context = brew_exts.BrewContext(mock_args)
requirements, containers = parse_requirements_from_xml(tool_xml)
for recipe_context in brew_util.requirements_to_recipe_contexts(
requirements, brew_context):
brew_exts.versioned_install(recipe_context)