Merge branch 'submission' into 'main'

Add deeplabcut Singularity recipe

See merge request !9

.gitlab-ci.yml

@@ -57,7 +57,16 @@ image:
 #    TAG: 0119cv6
 #    RECIPE_PATH: recipes/quality-control/fastqc/
 
+#####################
+# DeepLabCut
+#####################
 
+deeplabcut-2202-test:
+  extends: .templateTest
+  variables:
+    BASENAME: deeplabcut
+    TAG: 2202
+    RECIPE_PATH: recipes/image-analysis/deeplabcut
 
 #####################
 ## Quality control
@@ -68,7 +77,7 @@ fastqc-0119cv7-builddeploy:
   variables:
     BASENAME: fastqc
     TAG: 0119cv7
-    RECIPE_PATH: recipes/quality-control/fastqc/
+    RECIPE_PATH: recipes/quality-control/fastqc
   only:
     changes:
       - recipes/quality-control/fastqc/Singularity.fastqc-0119cv7
@@ -79,7 +88,7 @@ fastqc-0119cv8-builddeploy:
   variables:
     BASENAME: fastqc
     TAG: 0119cv8
-    RECIPE_PATH: recipes/quality-control/fastqc/
+    RECIPE_PATH: recipes/quality-control/fastqc
   only:
     changes:
       - recipes/quality-control/fastqc/Singularity.fastqc-0119cv8
@@ -89,7 +98,7 @@ fastqc-0119cv6-builddeploy:
   variables:
     BASENAME: fastqc
     TAG: 0119cv6
-    RECIPE_PATH: recipes/quality-control/fastqc/
+    RECIPE_PATH: recipes/quality-control/fastqc
   only:
     changes:
       - recipes/quality-control/fastqc/Singularity.fastqc-0119cv6

recipes/image-analysis/deeplabcut/Singularity.deeplabcut-2202

+Bootstrap: docker
+From: deeplabcut/deeplabcut:latest-core
+
+%help
+  A Singularity image from the deeplabcut:latest-core Docker. It comes with ResNet weights embedded. Deeplabcut 2.2.0.2
+
+%labels
+  AUTHOR Francesco Tabaro
+  VERSION 0.1
+  DEEPLABCUT_VERSION 2.2.0.2
+
+%post
+  apt-get update && apt-get install -y curl
+
+  cd /usr/local/lib/python3.8/dist-packages/deeplabcut/pose_estimation_tensorflow/models/pretrained/
+  
+  # Adapted from download.sh
+  for i in resnet_v1_50_2016_08_28.tar.gz resnet_v1_101_2016_08_28.tar.gz resnet_v1_152_2016_08_28.tar.gz; do 
+    curl -O http://download.tensorflow.org/models/$i
+    FN=$(tar xzvf $i)
+    chmod 666 $FN
+    rm $i
+  done
+
+%runscript
+  exec /usr/bin/python3 "$@"
+