From 0826538bffbe4bdb189768b15aaf61d3d19f79b7 Mon Sep 17 00:00:00 2001
From: Francesco Tabaro <francesco.tabaro@embl.it>
Date: Wed, 13 Apr 2022 18:35:06 +0000
Subject: [PATCH] Add deeplabcut Singularity recipe
---
.gitlab-ci.yml | 15 ++++++++---
.../deeplabcut/Singularity.deeplabcut-2202 | 27 +++++++++++++++++++
2 files changed, 39 insertions(+), 3 deletions(-)
create mode 100644 recipes/image-analysis/deeplabcut/Singularity.deeplabcut-2202
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index ee8f2a7..ae4ef4f 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 0000000..6c885aa
--- /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 $i
+ done
+
+%runscript
+ exec /usr/bin/python3 "$@"
+
--
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