diff --git a/config/galaxy.ini.sample b/config/galaxy.ini.sample index 5e1b6cb50ab..cc3f972e04e 100644 --- a/config/galaxy.ini.sample +++ b/config/galaxy.ini.sample @@ -202,8 +202,6 @@ paste.app_factory = galaxy.web.buildapp:app_factory # Set to True to instruct Galaxy to look for and install missing tool # dependencies before each job runs. #conda_auto_install = False -# Set to True to perform additional checking of installed Conda environment -#conda_verbose_install_check=False # Set to True to instruct Galaxy to install Conda from the web automatically # if it cannot find a local copy and conda_exec is not configured. #conda_auto_init = False diff --git a/lib/galaxy/tools/deps/conda_util.py b/lib/galaxy/tools/deps/conda_util.py index 7240754ca4f..e4a0cccda02 100644 --- a/lib/galaxy/tools/deps/conda_util.py +++ b/lib/galaxy/tools/deps/conda_util.py @@ -359,34 +359,20 @@ def is_target_available(conda_target, conda_context=None): return False -def is_conda_target_installed(conda_target, conda_context=None, verbose_install_check=False): +def is_conda_target_installed(conda_target, conda_context=None): conda_context = _ensure_conda_context(conda_context) # fail by default - success = False if conda_context.has_env(conda_target.install_environment): - if not verbose_install_check: - return True - # because export_list directs output to a file we - # need to make a temporary file, not use StringIO - f, package_list_file = tempfile.mkstemp(suffix='.env_packages') - os.close(f) - conda_context.export_list(conda_target.install_environment, package_list_file) - search_pattern = conda_target.package_specifier + '=' - with open(package_list_file) as input_file: - for line in input_file: - if line.startswith(search_pattern): - success = True - break - os.remove(package_list_file) - return success + return True + else: + return False -def filter_installed_targets(conda_targets, conda_context=None, verbose_install_check=False): +def filter_installed_targets(conda_targets, conda_context=None): conda_context = _ensure_conda_context(conda_context) installed = functools.partial(is_conda_target_installed, - conda_context=conda_context, - verbose_install_check=verbose_install_check) - return filter(installed, conda_targets) + conda_context=conda_context) + return list(filter(installed, conda_targets)) def build_isolated_environment( diff --git a/lib/galaxy/tools/deps/resolvers/conda.py b/lib/galaxy/tools/deps/resolvers/conda.py index f94cc015692..13477f77100 100644 --- a/lib/galaxy/tools/deps/resolvers/conda.py +++ b/lib/galaxy/tools/deps/resolvers/conda.py @@ -71,7 +71,6 @@ class CondaDependencyResolver(DependencyResolver, ListableDependencyResolver, In conda_exec = get_option("exec") debug = _string_as_bool(get_option("debug")) - verbose_install_check = _string_as_bool(get_option("verbose_install_check")) ensure_channels = get_option("ensure_channels") use_path_exec = get_option("use_path_exec") if use_path_exec is None: @@ -99,7 +98,6 @@ class CondaDependencyResolver(DependencyResolver, ListableDependencyResolver, In self.ensure_conda_installed() self.auto_install = auto_install self.copy_dependencies = copy_dependencies - self.verbose_install_check = verbose_install_check def ensure_conda_installed(self): """ @@ -149,7 +147,7 @@ class CondaDependencyResolver(DependencyResolver, ListableDependencyResolver, In conda_target = CondaTarget(name, version=version) is_installed = is_conda_target_installed( - conda_target, conda_context=self.conda_context, verbose_install_check=self.verbose_install_check + conda_target, conda_context=self.conda_context ) job_directory = kwds.get("job_directory", None) @@ -220,7 +218,7 @@ class CondaDependencyResolver(DependencyResolver, ListableDependencyResolver, In conda_target = CondaTarget(name, version=version) is_installed = is_conda_target_installed( - conda_target, conda_context=self.conda_context, verbose_install_check=self.verbose_install_check + conda_target, conda_context=self.conda_context ) if is_installed: @@ -232,7 +230,7 @@ class CondaDependencyResolver(DependencyResolver, ListableDependencyResolver, In else: # Recheck if installed is_installed = is_conda_target_installed( - conda_target, conda_context=self.conda_context, verbose_install_check=self.verbose_install_check + conda_target, conda_context=self.conda_context ) if not is_installed: log.debug("Removing failed conda install of {}, version '{}'".format(name, version))