cellpose-2.0.5-test

.gitlab-ci.yml

@@ -35,6 +35,12 @@ image:
 #####################
 
 ## WRITE YOUR TEST RULE HERE AFTER BRANCHING ON SUBMISSION AND CREATE A MERGE REQUEST
+cellpose-2.0.5-test:
+  extends: .templateTest
+  variables:
+    BASENAME: cellpose
+    TAG: 2.0.5
+    RECIPE_PATH: recipes/image-analysis/cellpose
 
 
 #####################

recipes/image-analysis/cellpose/Singularity.cellpose-2.0.5

+BootStrap: docker
+From: python:3.8-slim
+IncludeCmd: yes
+
+
+%labels
+	MAINTAINER=Yi Sun
+	Description=This receipe is used for cellpose galaxy tool
+	
+
+%runscript
+	OCI_ENTRYPOINT=''
+	OCI_CMD='"python3"'
+	CMDLINE_ARGS=""
+	for arg in "$@"; do
+    	CMDLINE_ARGS="${CMDLINE_ARGS} \"$arg\""
+	done
+
+	if [ -z "$OCI_CMD" ] && [ -n "$OCI_ENTRYPOINT" ]; then
+    		if [ $# -gt 0 ]; then
+        		SINGULARITY_OCI_RUN="${OCI_ENTRYPOINT} ${CMDLINE_ARGS}"
+    		else
+        		SINGULARITY_OCI_RUN="${OCI_ENTRYPOINT}"
+    		fi
+	fi
+
+	if [ -n "$OCI_CMD" ] && [ -z "$OCI_ENTRYPOINT" ]; then
+    		if [ $# -gt 0 ]; then
+        		SINGULARITY_OCI_RUN="${CMDLINE_ARGS}"
+    		else
+        		SINGULARITY_OCI_RUN="${OCI_CMD}"
+    		fi
+	fi
+
+	if [ $# -gt 0 ]; then
+    		SINGULARITY_OCI_RUN="${OCI_ENTRYPOINT} ${CMDLINE_ARGS}"
+	else
+    		SINGULARITY_OCI_RUN="${OCI_ENTRYPOINT} ${OCI_CMD}"
+	fi
+
+	eval "set ${SINGULARITY_OCI_RUN}"
+	exec "$@"
+
+%environment
+ 	NUMBA_CACHE_DIR=/tmp
+
+%post
+   	apt-get update -qq && \
+   	apt-get install -y -q --no-install-recommends \
+            gcc \
+            python3-dev \
+            python3-pip \
+            python3-wheel \
+            libblas-dev \
+            liblapack-dev \
+            libatlas-base-dev \
+            gfortran \
+            apt-utils \
+            bzip2 \
+            ca-certificates \
+            curl \
+            locales \
+            unzip && \
+   	apt-get clean && \
+   	rm -rf /var/lib/apt/lists/* 
+
+   	sed -i '/en_US.UTF-8/s/^# //g' /etc/locale.gen && locale-gen
+
+ 	pip install -U pip
+ 	pip install numpy numba>=0.43.1
+ 	pip install wheel scipy
+ 	pip install --no-cache-dir PyQt5 PyQt5.sip torch>=1.6 opencv-python-headless pyqtgraph>=0.11.0rc0 natsort google-cloud-storage 
+
+ 	pip install -U scikit-image matplotlib
+ 	pip install scikit-learn tqdm tifffile fastremap 
+ 	pip install cellpose==2.0.5
+
+
+