def _install_galaxy_config(tool_env, bin_dirs, env_vars):
"""
Setup galaxy tool config files (env.sh-es) and default version
symbolic links.
"""
install_dir = tool_env["system_install"]
env_path = os.path.join(install_dir, "env.sh")
bin_paths = [os.path.join(install_dir, bin_dir) for bin_dir in bin_dirs]
path_pieces = [bin_path for bin_path in bin_paths if exists(bin_path)]
if len(path_pieces) > 0 and not exists(env_path):
path_addtion = ":".join(path_pieces)
# Standard bin install, just add it to path
sudo("echo 'PATH=%s:$PATH' > %s" % (path_addtion, env_path))
venv_path = "%s/%s" % (install_dir, "venv")
if exists(venv_path):
# Have env.sh activate virtualdirectory
sudo("echo '. %s/bin/activate' >> %s" % (venv_path, env_path))
sudo("chmod +x %s" % env_path)
for env_var, env_var_value in env_vars.iteritems():
env_var_template = Template(env_var_value)
expanded_env_var_value = env_var_template.substitute(tool_env)
sudo("echo 'export %s=%s' >> %s" %
(env_var, expanded_env_var_value, env_path))
env.logger.debug("Added Galaxy env.sh file: %s" % env_path)
_set_default_config(tool_env, install_dir)
if _read_boolean(tool_env, "autoload_galaxy_tools",
False) and exists(env_path):
# In this case, the web user (e.g. ubuntu) should auto-load all of
# galaxy's default env.sh files so they are available for direct use
# as well.
_add_to_profiles(". %s" % env_path, profiles=["~/.bashrc"])
def _install_applications(env, tools_conf):
"""Install external tools (galaxy tool dependencies).
"""
applications = tools_conf["applications"] or {}
for (name, versions) in applications.iteritems():
if type(versions) is str:
versions = [versions]
for version_info in versions:
if type(version_info) is str:
_install_tool(env,
name,
version=version_info,
requirement_name=name)
else:
version = version_info["version"]
bin_dirs = version_info.get("bin_dirs", ["bin"])
env_vars = version_info.get("env_vars", {})
# Some requirements (e.g. blast+) maybe not have valid python
# identifiers as name. Use install_blast to setup but override
# requirement directory name with requirement_name field.
requirement_name = version_info.get("requirement_name", name)
tool_env = _install_tool(env,
name,
version,
bin_dirs=bin_dirs,
env_vars=env_vars,
requirement_name=requirement_name)
symlink_versions = version_info.get("symlink_versions", [])
if type(symlink_versions) is str:
symlink_versions = [symlink_versions]
for symlink_version in symlink_versions:
_set_default_config(tool_env, tool_env["system_install"],
symlink_version)
def _install_galaxy_config(tool_env, bin_dirs, env_vars):
"""
Setup galaxy tool config files (env.sh-es) and default version
symbolic links.
"""
install_dir = tool_env["system_install"]
env_path = os.path.join(install_dir, "env.sh")
bin_paths = [os.path.join(install_dir, bin_dir) for bin_dir in bin_dirs]
path_pieces = [bin_path for bin_path in bin_paths if env.safe_exists(bin_path)]
if len(path_pieces) > 0 and not env.safe_exists(env_path):
path_addtion = ":".join(path_pieces)
# Standard bin install, just add it to path
env.safe_sudo("echo 'PATH=%s:$PATH' > %s" % (path_addtion, env_path))
venv_path = "%s/%s" % (install_dir, "venv")
if env.safe_exists(venv_path):
# Have env.sh activate virtualdirectory
env.safe_sudo("echo '. %s/bin/activate' >> %s" % (venv_path, env_path))
env.safe_sudo("chmod +x %s" % env_path)
for env_var, env_var_value in env_vars.iteritems():
env_var_template = Template(env_var_value)
expanded_env_var_value = env_var_template.substitute(tool_env)
env.safe_sudo("echo 'export %s=%s' >> %s" % (env_var, expanded_env_var_value, env_path))
env.logger.debug("Added Galaxy env.sh file: %s" % env_path)
# TODO: If a direct install (i.e. tool_install_dir specified instead of galaxy_tools_dir)
# default is still setup. This is not really desired.
_set_default_config(tool_env, install_dir)
if _read_boolean(tool_env, "autoload_galaxy_tools", False) and env.safe_exists(env_path):
# In this case, the web user (e.g. ubuntu) should auto-load all of
# galaxy's default env.sh files so they are available for direct use
# as well.
_add_to_profiles(". %s" % env_path, profiles=["~/.bashrc"])
def _install_application(name, versions, tool_install_dir=None):
"""
Install single custom tool as Galaxy dependency application.
TODO: Rename versions and document options.
"""
if type(versions) is str:
versions = [versions]
for version_info in versions:
if type(version_info) is str:
_install_tool(env,
name,
version=version_info,
requirement_name=name,
tool_install_dir=tool_install_dir)
else:
version = version_info["version"]
bin_dirs = version_info.get("bin_dirs", ["bin"])
env_vars = version_info.get("env_vars", {})
provides = version_info.get("provides", [])
if isinstance(provides, (str, unicode, six.string_types)):
provides = [provides]
for provide_conf in provides[:]:
if isinstance(provide_conf, dict):
provides.remove(provide_conf)
if __check_conditional(provide_conf):
provies.append(provide_conf["name"])
# Some requirements (e.g. blast+) maybe not have valid python
# identifiers as name. Use install_blast to setup but override
# requirement directory name with requirement_name field.
requirement_name = version_info.get("requirement_name", name)
tool_env = _install_tool(env,
name,
version,
bin_dirs=bin_dirs,
env_vars=env_vars,
requirement_name=requirement_name,
tool_install_dir=tool_install_dir)
symlink_versions = version_info.get("symlink_versions", [])
if type(symlink_versions) is str:
symlink_versions = [symlink_versions]
for symlink_version in symlink_versions:
_set_default_config(tool_env, tool_env["system_install"],
symlink_version)
if provides:
install_dir = tool_env["system_install"]
## Create additional symlinked packages from this one.
tool_dir = "%s/.." % install_dir
tools_dir = "%s/.." % tool_dir
for package in provides:
link_dir = "%s/%s" % (tools_dir, package)
env.safe_sudo("ln -f -s '%s' '%s'" %
(requirement_name, link_dir))
def _install_galaxy_config(tool_env):
"""
Setup galaxy tool config files (env.sh-es) and default version
symbolic links.
"""
install_dir = tool_env["system_install"]
bin_dir = os.path.join(install_dir, "bin")
env_path = os.path.join(install_dir, "env.sh")
if exists(bin_dir) and not exists(env_path):
# Standard bin install, just add it to path
sudo("echo 'PATH=%s/bin:$PATH' > %s/env.sh" % (install_dir, install_dir))
sudo("chmod +x %s/env.sh" % install_dir)
_set_default_config(tool_env, install_dir)
def _install_application(name, versions, tool_install_dir=None):
"""
Install single custom tool as Galaxy dependency application.
TODO: Rename versions and document options.
"""
if type(versions) is str:
versions = [versions]
for version_info in versions:
if type(version_info) is str:
_install_tool(env, name, version=version_info, requirement_name=name, tool_install_dir=tool_install_dir)
else:
version = version_info["version"]
bin_dirs = version_info.get("bin_dirs", ["bin"])
env_vars = version_info.get("env_vars", {})
provides = version_info.get("provides", [])
if isinstance(provides, (str, unicode, basestring)):
provides = [provides]
for provide_conf in provides[:]:
if isinstance(provide_conf, dict):
provides.remove(provide_conf)
if __check_conditional(provide_conf):
provies.append(provide_conf["name"])
# Some requirements (e.g. blast+) maybe not have valid python
# identifiers as name. Use install_blast to setup but override
# requirement directory name with requirement_name field.
requirement_name = version_info.get("requirement_name", name)
tool_env = _install_tool(
env,
name,
version,
bin_dirs=bin_dirs,
env_vars=env_vars,
requirement_name=requirement_name,
tool_install_dir=tool_install_dir,
)
symlink_versions = version_info.get("symlink_versions", [])
if type(symlink_versions) is str:
symlink_versions = [symlink_versions]
for symlink_version in symlink_versions:
_set_default_config(tool_env, tool_env["system_install"], symlink_version)
if provides:
install_dir = tool_env["system_install"]
## Create additional symlinked packages from this one.
tool_dir = "%s/.." % install_dir
tools_dir = "%s/.." % tool_dir
for package in provides:
link_dir = "%s/%s" % (tools_dir, package)
env.safe_sudo("ln -f -s '%s' '%s'" % (requirement_name, link_dir))
def _install_galaxy_config(tool_env):
"""
Setup galaxy tool config files (env.sh-es) and default version
symbolic links.
"""
install_dir = tool_env["system_install"]
bin_dir = os.path.join(install_dir, "bin")
env_path = os.path.join(install_dir, "env.sh")
if exists(bin_dir) and not exists(env_path):
# Standard bin install, just add it to path
sudo("echo 'PATH=%s/bin:$PATH' > %s/env.sh" %
(install_dir, install_dir))
sudo("chmod +x %s/env.sh" % install_dir)
_set_default_config(tool_env, install_dir)
def _install_galaxy_config(tool_env, bin_dirs):
"""
Setup galaxy tool config files (env.sh-es) and default version
symbolic links.
"""
install_dir = tool_env["system_install"]
env_path = os.path.join(install_dir, "env.sh")
bin_paths = [os.path.join(install_dir, bin_dir) for bin_dir in bin_dirs]
path_pieces = [bin_path for bin_path in bin_paths if exists(bin_path)]
if len(path_pieces) > 0 and not exists(env_path):
path_addtion = ":".join(path_pieces)
# Standard bin install, just add it to path
sudo("echo 'PATH=%s:$PATH' > %s/env.sh" % (path_addtion, install_dir))
sudo("chmod +x %s/env.sh" % install_dir)
_set_default_config(tool_env, install_dir)
def _install_applications(env, tools_conf):
"""Install external tools (galaxy tool dependencies).
"""
applications = tools_conf["applications"] or {}
for (name, versions) in applications.iteritems():
if type(versions) is str:
versions = [versions]
for version_info in versions:
if type(version_info) is str:
_install_tool(env,
name,
version=version_info,
requirement_name=name)
else:
version = version_info["version"]
bin_dirs = version_info.get("bin_dirs", ["bin"])
env_vars = version_info.get("env_vars", {})
provides = version_info.get("provides", [])
if isinstance(provides, (str, unicode, basestring)):
provides = [provides]
# Some requirements (e.g. blast+) maybe not have valid python
# identifiers as name. Use install_blast to setup but override
# requirement directory name with requirement_name field.
requirement_name = version_info.get("requirement_name", name)
tool_env = _install_tool(env,
name,
version,
bin_dirs=bin_dirs,
env_vars=env_vars,
requirement_name=requirement_name)
symlink_versions = version_info.get("symlink_versions", [])
if type(symlink_versions) is str:
symlink_versions = [symlink_versions]
for symlink_version in symlink_versions:
_set_default_config(tool_env, tool_env["system_install"],
symlink_version)
if provides:
install_dir = tool_env["system_install"]
## Create additional symlinked packages from this one.
tool_dir = "%s/.." % install_dir
tools_dir = "%s/.." % tool_dir
for package in provides:
link_dir = "%s/%s" % (tools_dir, package)
env.safe_sudo("ln -f -s '%s' '%s'" %
(requirement_name, link_dir))
def _install_applications(env, tools_conf):
"""Install external tools (galaxy tool dependencies).
"""
applications = tools_conf["applications"] or {}
for (name, versions) in applications.iteritems():
if type(versions) is str:
versions = [versions]
for version_info in versions:
if type(version_info) is str:
_install_tool(env, name, version_info)
else:
version = version_info["version"]
bin_dirs = version_info.get("bin_dirs", ["bin"])
tool_env = _install_tool(env, name, version, bin_dirs)
symlink_versions = version_info.get("symlink_versions", [])
if type(symlink_versions) is str:
symlink_versions = [symlink_versions]
for symlink_version in symlink_versions:
_set_default_config(tool_env, tool_env["system_install"], symlink_version)
def _install_applications(env, tools_conf):
"""Install external tools (galaxy tool dependencies).
"""
applications = tools_conf["applications"] or {}
for (name, versions) in applications.iteritems():
if type(versions) is str:
versions = [versions]
for version_info in versions:
if type(version_info) is str:
_install_tool(env, name, version=version_info, requirement_name=name)
else:
version = version_info["version"]
bin_dirs = version_info.get("bin_dirs", ["bin"])
env_vars = version_info.get("env_vars", {})
provides = version_info.get("provides", [])
if isinstance(provides, (str, unicode, basestring)):
provides = [provides]
# Some requirements (e.g. blast+) maybe not have valid python
# identifiers as name. Use install_blast to setup but override
# requirement directory name with requirement_name field.
requirement_name = version_info.get("requirement_name", name)
tool_env = _install_tool(env, name, version, bin_dirs=bin_dirs, env_vars=env_vars, requirement_name=requirement_name)
symlink_versions = version_info.get("symlink_versions", [])
if type(symlink_versions) is str:
symlink_versions = [symlink_versions]
for symlink_version in symlink_versions:
_set_default_config(tool_env, tool_env["system_install"], symlink_version)
if provides:
install_dir = tool_env["system_install"]
## Create additional symlinked packages from this one.
tool_dir = "%s/.." % install_dir
tools_dir = "%s/.." % tool_dir
for package in provides:
link_dir = "%s/%s" % (tools_dir, package)
env.safe_sudo("ln -f -s '%s' '%s'" % (requirement_name, link_dir))
def _install_applications(env, tools_conf):
"""Install external tools (galaxy tool dependencies).
"""
applications = tools_conf["applications"] or {}
for (name, versions) in applications.iteritems():
if type(versions) is str:
versions = [versions]
for version_info in versions:
if type(version_info) is str:
_install_tool(env, name, version=version_info, requirement_name=name)
else:
version = version_info["version"]
bin_dirs = version_info.get("bin_dirs", ["bin"])
env_vars = version_info.get("env_vars", {})
# Some requirements (e.g. blast+) maybe not have valid python
# identifiers as name. Use install_blast to setup but override
# requirement directory name with requirement_name field.
requirement_name = version_info.get("requirement_name", name)
tool_env = _install_tool(env, name, version, bin_dirs=bin_dirs, env_vars=env_vars, requirement_name=requirement_name)
symlink_versions = version_info.get("symlink_versions", [])
if type(symlink_versions) is str:
symlink_versions = [symlink_versions]
for symlink_version in symlink_versions:
_set_default_config(tool_env, tool_env["system_install"], symlink_version)
def _update_default(env, install_dir):
sudo("touch %s/env.sh" % install_dir)
sudo("chmod +x %s/env.sh" % install_dir)
_set_default_config(env, install_dir)
def _update_default(env, install_dir):
sudo("touch %s/env.sh" % install_dir)
sudo("chmod +x %s/env.sh" % install_dir)
_set_default_config(env, install_dir)
