diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index ee8f2a7f14f35b690dda9c285de411bf1f759a4f..ae4ef4f9afa96c5a99b48f6cc73ad7fe6630b3c6 100644 --- a/.gitlab-ci.yml +++ b/.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 diff --git a/recipes/image-analysis/deeplabcut/Singularity.deeplabcut-2202 b/recipes/image-analysis/deeplabcut/Singularity.deeplabcut-2202 new file mode 100644 index 0000000000000000000000000000000000000000..6c885aa10a959421cef265737fcbc543fb4ff9ab --- /dev/null +++ b/recipes/image-analysis/deeplabcut/Singularity.deeplabcut-2202 @@ -0,0 +1,27 @@ +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 $i + done + +%runscript + exec /usr/bin/python3 "$@" +