singularity build: automatically try fakeroot mode if proot is missing

common-workflow-language · Dec 5, 2023 · 7e1b082 · 7e1b082
1 parent 9d7eacb
commit 7e1b082
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diff --git a/cwltool/singularity.py b/cwltool/singularity.py
@@ -186,7 +186,13 @@ def get_image(
                 file.write(singularityfile)
 
             os.environ["APPTAINER_TMPDIR"] = absolute_path
-            Client.build(recipe=singularityfile_path, build_folder=absolute_path, sudo=False)
+            singularity_options = ["--fakeroot"] if not shutil.which("proot") else []
+            Client.build(
+                recipe=singularityfile_path,
+                build_folder=absolute_path,
+                sudo=False,
+                options=singularity_options,
+            )
             found = True
         elif "dockerImageId" not in dockerRequirement and "dockerPull" in dockerRequirement:
             match = re.search(pattern=r"([a-z]*://)", string=dockerRequirement["dockerPull"])

diff --git a/tox.ini b/tox.ini
@@ -40,6 +40,7 @@ passenv =
   GITHUB_*
   PROOT_NO_SECCOMP
   APPTAINER_TMPDIR
+  SINGULARITY_FAKEROOT
 
 extras =
   py3{8,9,10,11,12}-unit: deps