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 __init__(self, **kwds):
"""Construct a postgres database source from planemo configuration."""
self.psql_path = 'psql'
self.database_user = '******'
self.database_password = DEFAULT_POSTGRES_PASSWORD
self.database_host = 'localhost' # TODO: Make docker host
self.database_port = DEFAULT_POSTGRES_PORT_EXPOSE
self._kwds = kwds
self._docker_host_kwds = dockerfiles.docker_host_args(**kwds)
if not is_running_container(**self._docker_host_kwds):
start_postgres_docker(**self._docker_host_kwds)
# Hack to give docker a bit of time to boot up and allow psql to start.
time.sleep(30)
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)