Organize all singularity definitions into vm directory

README.md

@@ -12,7 +12,7 @@ This repository uses both Pytorch and Tensorflow Serving (TFS).
 This repository supports both Docker and Singularity environments. 
 
 The dockerfile is provided at the root of the repository ([Dockerfile](Dockerfile)), and the singularity 
-definition file is in the `vm` folder ([singularity.def](vm/singularity.def)).
+definition file is in the `vm` folder ([singularity.def](vm/runtime.def)).
 
 To learn more about how we support this, please read [vm/README.md](vm/README.md).
 

support_code/RBase.def → vm/RBase.def

@@ -1,11 +1,14 @@
+# build like:
+#   singularity build RBase.sif vm/RBase.def
+
 Bootstrap: docker
 From:rocker/tidyverse:4.4.2
 
 %setup
         mkdir -p ${SINGULARITY_ROOTFS}/mouse-tracking-runtime/support_code/
 
 %files
-        behavior_summaries.R /mouse-tracking-runtime/support_code/.
+        support_code/behavior_summaries.R /mouse-tracking-runtime/support_code/.
 
 %post
         apt-get update
@@ -19,4 +22,3 @@ From:rocker/tidyverse:4.4.2
         apt-get install -y libnlopt-dev 
         apt-get install -y build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev libgit2-dev
         Rscript -e 'install.packages(c("usethis","devtools","optparse"), repos="https://cran.rstudio.com")'
-

vm/README.md

@@ -47,7 +47,7 @@ The Singularity container:
 ### Building Singularity Images
 
 ```bash
-singularity build mouse-tracking-runtime.sif vm/singularity.def
+singularity build mouse-tracking-runtime.sif vm/runtime.def
 ```
 
 ## Framework Compatibility
@@ -75,7 +75,7 @@ docker run --gpus all mouse-tracking-runtime mouse-tracking-runtime --help
 ### Singularity
 ```bash
 # Build and run the Singularity container
-singularity build mouse-tracking-runtime.sif vm/singularity.def
+singularity build mouse-tracking-runtime.sif vm/runtime.def
 singularity run --nv mouse-tracking-runtime.sif mouse-tracking-runtime --help
 ```
 

vm/singularity.def → vm/runtime.def

@@ -1,11 +1,5 @@
-# build like:
-#   singularity build mouse-tracking-runtime.sif singularity.def
-
 Bootstrap: docker
 From: aberger4/mouse-tracking:python3.10-slim
 
 %setup
     mkdir -p ${SINGULARITY_ROOTFS}/workspace/models/
-
-%files
-    ./models /workspace/

support_code/sleap-1.4.1.def → vm/sleap-1.4.1.def

@@ -1,11 +1,14 @@
+# build like:
+#   singularity build sleap-1.4.1.sif vm/sleap-1.4.1.def
+
 Bootstrap: docker
 from: ubuntu:22.04
 
 %setup
 	mkdir -p ${SINGULARITY_ROOTFS}/mouse-tracking-runtime/support_code/
 
 %files
-	static-object-correct.py /mouse-tracking-runtime/support_code/.
+	support_code/static-object-correct.py /mouse-tracking-runtime/support_code/.
 
 %post
 	apt-get update

support_code/sleap-io-0.2.0.def → vm/sleap-io-0.2.0.def

@@ -1,11 +1,14 @@
+# build like:
+#   singularity build sleap-io-0.2.0.sif vm/sleap-io-0.2.0.def
+
 Bootstrap: docker
 from: python:3.10-bookworm
 
 %setup
 	mkdir -p ${SINGULARITY_ROOTFS}/mouse-tracking-runtime/support_code/
 
 %files
-	static-object-correct.py /mouse-tracking-runtime/support_code/.
+	support_code/static-object-correct.py /mouse-tracking-runtime/support_code/.
 
 %post
 	apt-get update