changeset 7:7a415a2ea490 draft

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 597cb3dc531963d02c5db0e4fc2596fcb06728dd

--- a/creators.xml	Wed Apr 24 08:13:34 2024 +0000
+++ b/creators.xml	Wed Dec 17 22:28:37 2025 +0000
@@ -5,6 +5,16 @@
         <yield />
     </xml>
 
+    <xml name="creators/kostrykin">
+        <person givenName="Leonid" familyName="Kostrykin"/>
+        <yield/>
+    </xml>
+
+    <xml name="creators/rmassei">
+        <person givenName="Riccardo" familyName="Massei"/>
+        <yield/>
+    </xml>
+
     <xml name="creators/alliecreason">
         <person givenName="Allison" familyName="Creason"/>
         <yield/>
@@ -19,5 +29,15 @@
         <person givenName="Till" familyName="Korten"/>
         <yield/>
     </xml>
-    
+
+    <xml name="creators/pavanvidem">
+        <person givenName="Pavan" familyName="Videm"/>
+        <yield/>
+    </xml>
+
+    <xml name="creators/tuncK">
+        <person givenName="Tunc" familyName="Kayikcioglu"/>
+        <yield/>
+    </xml>
+
 </macros>

--- a/run-superdsm.py	Wed Apr 24 08:13:34 2024 +0000
+++ b/run-superdsm.py	Wed Dec 17 22:28:37 2025 +0000
@@ -86,10 +86,12 @@
     import superdsm.io
     import superdsm.render
 
-    ray.init(num_cpus=num_processes, log_to_driver=True)
+    # The explicit `dir` and `prefix` is to avoid breaking the 107 byte limit for socket paths in Biocontainers
+    # See for details: https://github.com/BMCV/galaxy-image-analysis/pull/178
+    with tempfile.TemporaryDirectory(dir='/tmp', prefix='superdsm') as tmpdirname:
+        tmpdir = pathlib.Path(tmpdirname)
+        ray.init(num_cpus=num_processes, log_to_driver=True, _temp_dir=str(tmpdir / 'ray'))
 
-    with tempfile.TemporaryDirectory() as tmpdirname:
-        tmpdir = pathlib.Path(tmpdirname)
         img_ext = imghdr.what(args.image)
         img_filepath = tmpdir / f'input.{img_ext}'
         shutil.copy(str(args.image), img_filepath)

--- a/superdsm.xml	Wed Apr 24 08:13:34 2024 +0000
+++ b/superdsm.xml	Wed Dec 17 22:28:37 2025 +0000
@@ -191,7 +191,7 @@
 
         SuperDSM is a globally optimal method for cell nuclei segmentation using deformable shape models and their inherent law of superadditivity.
 
-        You can either use an individual input image (PNG, TIF) or a collection of such images.
+        You can either use an individual input image (PNG, TIFF) or a collection of such images.
 
     </help>
     <citations>