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):
"""Launch shell in Docker container for a tool.
Will launch a shell in the Docker container referenced by the specified
tool. Prints a command to do this the way Galaxy would in job files it
generates - so be sure to wrap this in $(...) to launch the subshell.
\b
$ $(planemo docker_shell bowtie2.xml)
...
root@b8754062f875:/#
"""
tool_xml = load_tool(path)
requirements, containers = parse_requirements_from_xml(tool_xml)
identifier = None
for container in containers:
if container.type == "docker":
identifier = container.identifier
# Refactor mulled container resolver to be able to do this.
if kwds["from_tag"]:
identifier = "-t %s" % identifier
tool_dir = os.path.dirname(os.path.abspath(path))
working_dir = os.path.abspath(os.getcwd())
if tool_dir.startswith(working_dir):
volumes = ["%s:%s" % (working_dir, working_dir)]
elif working_dir.startswith(tool_dir):
volumes = ["%s:%s" % (tool_dir, tool_dir)]
else:
volumes = [
"%s:%s" % (working_dir, working_dir),
"%s:%s" % (tool_dir, tool_dir)
]
script = docker_util.build_docker_run_command(
"/bin/bash",
identifier,
interactive=True,
terminal=True,
working_directory=working_dir,
volumes=volumes,
**dockerfiles.docker_host_args(**kwds))
print(script)
def cli(ctx, path, brew=None):
"""Install tool requirements using brew.
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)
def dockerfile_build(path, dockerfile=None, error=log.error, **kwds):
expected_container_names = set()
tool_directories = set()
for (tool_path, tool_xml) in load_tool_elements_from_path(path):
requirements, containers = parse_requirements_from_xml(tool_xml)
for container in containers:
if container.type == "docker":
expected_container_names.add(container.identifier)
tool_directories.add(os.path.dirname(tool_path))
break
if len(expected_container_names) == 0:
error("Could not find any docker identifiers to generate.")
if len(expected_container_names) > 1:
error(
"Multiple different docker identifiers found for selected tools [%s]",
expected_container_names)
image_identifier = expected_container_names.pop()
dockerfile = __find_dockerfile(dockerfile, tool_directories)
if dockerfile is not None:
docker_command_parts = docker_util.build_command(
image_identifier, dockerfile, **docker_host_args(**kwds))
else:
docker_command_parts = docker_util.build_pull_command(
image_identifier, **docker_host_args(**kwds))
commands.execute(docker_command_parts)
commands.execute(docker_command_parts)
docker_image_cache = kwds['docker_image_cache']
if docker_image_cache:
destination = docker_cache_path(docker_image_cache, image_identifier)
save_image_command_parts = docker_util.build_save_image_command(
image_identifier, destination, **docker_host_args(**kwds))
commands.execute(save_image_command_parts)
def parse_requirements_and_containers(self):
return requirements.parse_requirements_from_xml(self.root)
