def cli(ctx, path, **kwds):
"""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.::
% $(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
if kwds["from_tag"]:
identifier = "-t %s" % identifier
script = docker_util.build_docker_run_command(
"/bin/bash",
identifier,
interactive=True,
**dockerfiles.docker_host_args(**kwds)
)
print(script)
def cli(ctx, path, **kwds):
"""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.::
% $(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
if kwds["from_tag"]:
identifier = "-t %s" % identifier
script = docker_util.build_docker_run_command(
"/bin/bash",
identifier,
interactive=True,
**dockerfiles.docker_host_args(**kwds))
print(script)
def implementation(logger, args):
list_of_files = {}
if path_exists(args.sg_local_path, logger=logger, force=True):
for (dirpath, dirnames, filenames) in os.walk(args.sg_local_path):
for filename in filenames:
list_of_files[filename] = os.sep.join([dirpath, filename])
logger.debug(list_of_files)
gi = GalaxyInstance(args.url, key=args.key)
tools = gi.tools.get_tools()
counter_singularity = 0
counter_docker = 0
match = {}
unmatch = []
for t in tools:
t_id = t['id']
t_xml_file = gi.tools.show_tool(t['id'])['config_file']
container_name = None
try:
tool_xml = load(t_xml_file)
requirements, containers = parse_requirements_from_xml(tool_xml)
conda_targets = requirements_to_conda_targets(requirements)
mulled_targets = [
build_target(c.package, c.version) for c in conda_targets
]
container_name = mulled_container_name("biocontainers",
mulled_targets)
except Exception as ex:
logger.exception('Caught an error at {} with tid: {}'.format(
args.url, t_id))
pass
singularity = 'not_found'
if container_name:
container_name = container_name.lower()
counter_docker += 1
if os.path.basename(container_name) in list_of_files:
singularity = os.path.join(args.sg_local_path,
os.path.basename(container_name))
counter_singularity += 1
match[t_id] = {
'docker': "docker://{}".format(container_name),
'singularity': singularity
}
unmatch.append(t_id)
print(t_id, container_name, singularity)
dump(match, "{}_{}".format(args.url.split('/')[2], args.matched))
dump(unmatch, "{}_{}".format(args.url.split('/')[2], args.notmatched))
print("number of tools {}".format(len(tools)))
print("number of docker images matched {}".format(counter_docker))
print("number of singularity images in CVMFS {}".format(
len(list_of_files)))
print(
"number of singularity images matched {}".format(counter_singularity))
def collect_conda_targets(path, found_tool_callback=None, conda_context=None):
conda_targets = []
for (tool_path, tool_xml) in load_tool_elements_from_path(path):
if found_tool_callback:
found_tool_callback(tool_path)
requirements, containers = parse_requirements_from_xml(tool_xml)
conda_targets.extend(conda_util.requirements_to_conda_targets(requirements))
return conda_targets
def collect_conda_targets(path, found_tool_callback=None, conda_context=None):
conda_targets = []
for (tool_path, tool_xml) in load_tool_elements_from_path(path):
if found_tool_callback:
found_tool_callback(tool_path)
requirements, containers = parse_requirements_from_xml(tool_xml)
conda_targets.extend(conda_util.requirements_to_conda_targets(requirements))
return conda_targets
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, **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.::
% $(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
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. (**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)
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)
def parse_requirements_and_containers(self):
return requirements.parse_requirements_from_xml(self.root)
def parse_requirements_and_containers(self):
return requirements.parse_requirements_from_xml(self.root)
