Automatically initialize Apptainer

lib/galaxy/app.py

@@ -369,6 +369,7 @@ def _configure_toolbox(self):
             involucro_path=self.config.involucro_path,
             involucro_auto_init=self.config.involucro_auto_init,
             mulled_channels=self.config.mulled_channels,
+            apptainer_prefix=self.config.apptainer_prefix,
         )
         mulled_resolution_cache = None
         if self.config.mulled_resolution_cache_type:

lib/galaxy/config/schemas/config_schema.yml

@@ -399,6 +399,14 @@ mapping:
           This will prevent problems with some specific packages (perl, R), at the cost
           of extra disk space usage and extra time spent copying packages.
 
+      apptainer_prefix:
+        type: str
+        default: _apptainer
+        path_resolves_to: tool_dependency_dir
+        required: false
+        desc: |
+          Apptainer installation prefix.
+
       local_conda_mapping_file:
         type: str
         default: 'local_conda_mapping.yml'

lib/galaxy/jobs/__init__.py

@@ -109,6 +109,7 @@
 from galaxy.util.bunch import Bunch
 from galaxy.util.expressions import ExpressionContext
 from galaxy.util.path import external_chown
+from galaxy.util.properties import running_from_source
 from galaxy.util.xml_macros import load
 from galaxy.web_stack.handlers import ConfiguresHandlers
 from galaxy.work.context import WorkRequestContext
@@ -1162,6 +1163,22 @@ def cleanup_job(self):
     def requires_containerization(self):
         return util.asbool(self.get_destination_configuration("require_container", "False"))
 
+    @property
+    def use_metadata_venv(self):
+        return util.asbool(self.get_destination_configuration("use_metadata_venv", not running_from_source))
+
+    @property
+    def create_metadata_venv(self):
+        return util.asbool(self.get_destination_configuration("create_metadata_venv", self.use_metadata_venv))
+
+    @property
+    def metadata_venv_python(self):
+        return self.get_destination_configuration("metadata_venv_python", sys.executable)
+
+    @property
+    def metadata_venv_path(self):
+        return util.asbool(self.get_destination_configuration("metadata_venv_path", "False")) or None
+
     @property
     def use_metadata_binary(self):
         return util.asbool(self.get_destination_configuration("use_metadata_binary", "False"))

lib/galaxy/tool_util/deps/apptainer_util.py

@@ -0,0 +1,116 @@
+import logging
+import os
+import platform
+import tempfile
+from typing import (
+    List,
+    Optional,
+    Union,
+)
+
+import packaging.version
+
+from galaxy.util import (
+    commands,
+    download_to_file,
+)
+from . import installable
+
+DEFAULT_APPTAINER_COMMAND = "apptainer"
+APPTAINER_VERSION = "1.4.0"
+APPTAINER_URL_TEMPLATE = "https://github.com/galaxyproject/apptainer-build-unprivileged/releases/download/v{version}/apptainer-{version}-{el}-{arch}.tar.gz"
+
+
+log = logging.getLogger(__name__)
+
+
+def _glibc_version() -> Optional[packaging.version.Version]:
+    version = None
+    try:
+        # First line should always be 'ldd (dist-specific) VERSION'
+        glibc_version = commands.execute(["ldd", "--version"]).splitlines()[0].split()[-1]
+        version = packaging.version.parse(glibc_version)
+    except Exception as exc:
+        log.warning(f"Unable to get glibc version: {str(exc)}")
+    return version
+
+
+def apptainer_url() -> str:
+    glibc_version = _glibc_version()
+    el = "el8"
+    if glibc_version and glibc_version >= packaging.version.parse("2.34"):
+        el = "el9"
+    url = APPTAINER_URL_TEMPLATE.format(version=APPTAINER_VERSION, el=el, arch=platform.machine())
+    return url
+
+
+class ApptainerContext(installable.InstallableContext):
+    installable_description = "Apptainer"
+
+    def __init__(
+        self,
+        apptainer_prefix: Optional[str] = None,
+        apptainer_exec: Optional[Union[str, List[str]]] = None,
+    ) -> None:
+        self.apptainer_prefix = apptainer_prefix
+
+        if apptainer_exec and isinstance(apptainer_exec, str):
+            apptainer_exec = os.path.normpath(apptainer_exec)
+
+        if apptainer_exec is not None:
+            self.apptainer_exec = apptainer_exec
+        elif apptainer_prefix is not None:
+            self.apptainer_exec = os.path.join(apptainer_prefix, "bin", "apptainer")
+        else:
+            self.apptainer_exec = "apptainer"
+
+    def apptainer_version(self) -> str:
+        cmd = [self.apptainer_exec, "version"]
+        version_out = commands.execute(cmd).strip()
+        return version_out
+
+    def is_installed(self) -> bool:
+        try:
+            self.apptainer_version()
+            return True
+        except Exception:
+            return False
+
+    def can_install(self) -> bool:
+        if self.apptainer_prefix is None:
+            return False
+        if platform.system() != "Linux" or platform.machine() not in ("x86_64", "aarch64"):
+            return False
+        glibc_version = _glibc_version()
+        if not glibc_version or glibc_version < packaging.version.parse("2.28"):
+            return False
+        return True
+
+    @property
+    def parent_path(self) -> Optional[str]:
+        prefix = None
+        if self.apptainer_prefix:
+            prefix = os.path.dirname(os.path.abspath(self.apptainer_prefix))
+        return prefix
+
+
+def install_apptainer(apptainer_context: ApptainerContext) -> int:
+    with tempfile.NamedTemporaryFile(suffix=".tar.gz", prefix="apptainer_install", delete=False) as temp:
+        tarball_path = temp.name
+    install_cmd = ["tar", "zxf", tarball_path, "-C", apptainer_context.apptainer_prefix, "--strip-components=1"]
+    fetch_url = apptainer_url()
+    log.info("Installing Apptainer, this may take several minutes.")
+    log.info(f"Fetching from: {fetch_url}")
+    assert apptainer_context.apptainer_prefix
+    try:
+        os.makedirs(apptainer_context.apptainer_prefix)
+        download_to_file(fetch_url, tarball_path)
+        commands.execute(install_cmd)
+    except Exception:
+        log.exception("Failed to fetch Apptainer tarball")
+        return 1
+    finally:
+        if os.path.exists(tarball_path):
+            os.remove(tarball_path)
+    log.info(f"Apptainer installed to: {apptainer_context.apptainer_prefix}")
+    return 0

lib/galaxy/tool_util/deps/container_classes.py

@@ -532,8 +532,11 @@ class SingularityContainer(Container, HasDockerLikeVolumes):
     container_type = SINGULARITY_CONTAINER_TYPE
 
     def get_singularity_target_kwds(self) -> Dict[str, Any]:
+        cmd_default = (
+            self.container_description and self.container_description.cmd
+        ) or singularity_util.DEFAULT_SINGULARITY_COMMAND
         return dict(
-            singularity_cmd=self.prop("cmd", singularity_util.DEFAULT_SINGULARITY_COMMAND),
+            singularity_cmd=self.prop("cmd", cmd_default),
             sudo=asbool(self.prop("sudo", singularity_util.DEFAULT_SUDO)),
             sudo_cmd=self.prop("sudo_cmd", singularity_util.DEFAULT_SUDO_COMMAND),
         )