def startup_command(self, ctx, **kwds):
"""Return a shell command used to startup this instance.
Among other common planmo kwds, this should respect the
``daemon`` keyword.
"""
daemon = kwds.get("daemon", False)
daemon_str = "" if not daemon else " -d"
docker_run_extras = "-p %s:80%s" % (self.port, daemon_str)
env_directives = ["%s='%s'" % item for item in self.env.items()]
image = kwds.get("docker_galaxy_image", "bgruening/galaxy-stable")
run_command = docker_util.build_docker_run_command(
"",
image,
interactive=False,
env_directives=env_directives,
working_directory=None,
name=self.server_name,
run_extra_arguments=docker_run_extras,
set_user=False,
volumes=self.volumes,
**self.docker_target_kwds)
chmod_command = [
"chmod",
"-R",
"o+rwx",
self.config_directory,
]
if self.export_directory:
chmod_command.append(self.export_directory)
return shell_join(
argv_to_str(chmod_command),
run_command,
)
def startup_command(self, ctx, **kwds):
"""Return a shell command used to startup this instance.
Among other common planmo kwds, this should respect the
``daemon`` keyword.
"""
daemon = kwds.get("daemon", False)
daemon_str = "" if not daemon else " -d"
docker_run_extras = "-p %s:80%s" % (self.port, daemon_str)
env_directives = ["%s='%s'" % item for item in self.env.items()]
image = kwds.get("docker_galaxy_image", "bgruening/galaxy-stable")
run_command = docker_util.build_docker_run_command(
"", image,
interactive=False,
env_directives=env_directives,
working_directory=None,
name=self.server_name,
run_extra_arguments=docker_run_extras,
set_user=False,
volumes=self.volumes,
**self.docker_target_kwds
)
chmod_command = [
"chmod",
"-R",
"o+rwx",
self.config_directory,
]
if self.export_directory:
chmod_command.append(self.export_directory)
return shell_join(
argv_to_str(chmod_command),
run_command,
)
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 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)
