Python populate_galaxy_pathsの例

コード例 #1

ファイル: galaxy.py プロジェクト: blankenberg/cloudman

    def update_galaxy_config(self):
        """
        Update Galaxy application configuration.

        Optionally set Galaxy to use multiple processes, then populate dynamic
        options (i.e., arbitrary options coming from user data), adjust system
        paths and set admin users.
        """
        if self.multiple_processes():
            populate_process_options(self.option_manager)
        populate_dynamic_options(self.option_manager)
        populate_galaxy_paths(self.option_manager)
        populate_admin_users(self.option_manager)

コード例 #2

ファイル: galaxy.py プロジェクト: ddavidovic/cloudman

    def update_galaxy_config(self):
        """
        Update Galaxy application configuration.

        Optionally set Galaxy to use multiple processes, then populate dynamic
        options (i.e., arbitrary options coming from user data), adjust system
        paths and set admin users.
        """
        if self.multiple_processes():
            populate_process_options(self.option_manager)
        populate_dynamic_options(self.option_manager)
        populate_galaxy_paths(self.option_manager)
        populate_admin_users(self.option_manager)

コード例 #3

ファイル: test_galaxy_conf.py プロジェクト: nuwang/cloudman

def test_populate_galaxy_paths():
    app = TestApp()
    option_manager = TestOptionManager(app)
    populate_galaxy_paths(option_manager)
    main_options = option_manager.options["app:main"]
    assert main_options["genome_data_path"] == \
        join(TEST_INDICES_DIR, "genomes")
    assert main_options["len_file_path"] == \
        join(TEST_DATA_DIR, "configuration_data", "len")
    assert main_options["tool_dependency_dir"] == \
        join(TEST_TOOLS_DIR, "tools")
    assert main_options["file_path"] == \
        join(TEST_DATA_DIR, "files")
    assert main_options["new_file_path"] == \
        join(TEST_DATA_DIR, "tmp")
    assert main_options["job_working_directory"] == \
        join(TEST_DATA_DIR, "tmp", "job_working_directory")
    assert main_options["cluster_files_directory"] == \
        join(TEST_DATA_DIR, "tmp", "pbs")
    assert main_options["ftp_upload_dir"] == \
        join(TEST_DATA_DIR, "tmp", "ftp")
    assert main_options["nginx_upload_store"] == \
        join(TEST_DATA_DIR, "upload_store")

コード例 #4

ファイル: test_galaxy_conf.py プロジェクト: jmchilton/cloudman

def test_populate_galaxy_paths():
    app = TestApp()
    option_manager = TestOptionManager(app)
    populate_galaxy_paths(option_manager)
    main_options = option_manager.options["app:main"]
    assert main_options["genome_data_path"] == \
        join(TEST_INDICES_DIR, "genomes")
    assert main_options["len_file_path"] == \
        join(TEST_DATA_DIR, "configuration_data", "len")
    assert main_options["tool_dependency_dir"] == \
        join(TEST_TOOLS_DIR, "tools")
    assert main_options["file_path"] == \
        join(TEST_DATA_DIR, "files")
    assert main_options["new_file_path"] == \
        join(TEST_DATA_DIR, "tmp")
    assert main_options["job_working_directory"] == \
        join(TEST_DATA_DIR, "tmp", "job_working_directory")
    assert main_options["cluster_files_directory"] == \
        join(TEST_DATA_DIR, "tmp", "pbs")
    assert main_options["ftp_upload_dir"] == \
        join(TEST_DATA_DIR, "tmp", "ftp")
    assert main_options["nginx_upload_store"] == \
        join(TEST_DATA_DIR, "upload_store")

コード例 #5

ファイル: galaxy.py プロジェクト: jmchilton/cloudman

 def update_galaxy_config(self):
     if self._multiple_processes():
         populate_process_options(self.option_manager)
     populate_dynamic_options(self.option_manager)
     populate_galaxy_paths(self.option_manager)
     populate_admin_users(self.option_manager)