fix: installing iamgej in dockerfiles

PolusAI · Jun 28, 2024 · e84bec6 · e84bec6
1 parent 23b4e02
commit e84bec6
Show file tree

Hide file tree

Showing 31 changed files with 31 additions and 0 deletions.
diff --git a/clustering/k-means-clustering-tool/Dockerfile b/clustering/k-means-clustering-tool/Dockerfile
@@ -10,6 +10,7 @@ ENV POLUS_LOG="INFO"
 WORKDIR ${EXEC_DIR}
 
 # Initialize ImageJ
+pip3 install pyimagej==1.4.1 jpype1==1.5.0 scyjava==1.9.1 imglyb==2.1.0
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
 # TODO: Change the tool_dir to the tool directory

diff --git a/clustering/outlier-removal-tool/Dockerfile b/clustering/outlier-removal-tool/Dockerfile
@@ -10,6 +10,7 @@ ENV POLUS_LOG="INFO"
 WORKDIR ${EXEC_DIR}
 
 # Initialize ImageJ
+pip3 install pyimagej==1.4.1 jpype1==1.5.0 scyjava==1.9.1 imglyb==2.1.0
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
 # TODO: Change the tool_dir to the tool directory

diff --git a/features/feature-segmentation-eval-tool/Dockerfile b/features/feature-segmentation-eval-tool/Dockerfile
@@ -10,6 +10,7 @@ ENV POLUS_LOG="INFO"
 WORKDIR ${EXEC_DIR}
 
 # Initialize ImageJ
+pip3 install pyimagej==1.4.1 jpype1==1.5.0 scyjava==1.9.1 imglyb==2.1.0
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
 # TODO: Change the tool_dir to the tool directory

diff --git a/features/nyxus-tool/Dockerfile b/features/nyxus-tool/Dockerfile
@@ -10,6 +10,7 @@ ENV POLUS_LOG="INFO"
 WORKDIR ${EXEC_DIR}
 
 # Initialize ImageJ
+pip3 install pyimagej==1.4.1 jpype1==1.5.0 scyjava==1.9.1 imglyb==2.1.0
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
 # TODO: Change the tool_dir to the tool directory

diff --git a/features/pixel-segmentation-eval-tool/Dockerfile b/features/pixel-segmentation-eval-tool/Dockerfile
@@ -10,6 +10,7 @@ ENV POLUS_LOG="INFO"
 WORKDIR ${EXEC_DIR}
 
 # Initialize ImageJ
+pip3 install pyimagej==1.4.1 jpype1==1.5.0 scyjava==1.9.1 imglyb==2.1.0
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
 # TODO: Change the tool_dir to the tool directory

diff --git a/features/region-segmentation-eval-tool/Dockerfile b/features/region-segmentation-eval-tool/Dockerfile
@@ -10,6 +10,7 @@ ENV POLUS_LOG="INFO"
 WORKDIR ${EXEC_DIR}
 
 # Initialize ImageJ
+pip3 install pyimagej==1.4.1 jpype1==1.5.0 scyjava==1.9.1 imglyb==2.1.0
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
 # TODO: Change the tool_dir to the tool directory

diff --git a/formats/arrow-to-tabular-tool/Dockerfile b/formats/arrow-to-tabular-tool/Dockerfile
@@ -10,6 +10,7 @@ ENV POLUS_LOG="INFO"
 WORKDIR ${EXEC_DIR}
 
 # Initialize ImageJ
+pip3 install pyimagej==1.4.1 jpype1==1.5.0 scyjava==1.9.1 imglyb==2.1.0
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
 # TODO: Change the tool_dir to the tool directory

diff --git a/formats/file-renaming-tool/Dockerfile b/formats/file-renaming-tool/Dockerfile
@@ -10,6 +10,7 @@ ENV POLUS_LOG="INFO"
 WORKDIR ${EXEC_DIR}
 
 # Initialize ImageJ
+pip3 install pyimagej==1.4.1 jpype1==1.5.0 scyjava==1.9.1 imglyb==2.1.0
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
 # TODO: Change the tool_dir to the tool directory

diff --git a/formats/label-to-vector-tool/Dockerfile b/formats/label-to-vector-tool/Dockerfile
@@ -10,6 +10,7 @@ ENV POLUS_LOG="INFO"
 WORKDIR ${EXEC_DIR}
 
 # Initialize ImageJ
+pip3 install pyimagej==1.4.1 jpype1==1.5.0 scyjava==1.9.1 imglyb==2.1.0
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
 # TODO: Change the tool_dir to the tool directory

diff --git a/formats/ome-converter-tool/Dockerfile b/formats/ome-converter-tool/Dockerfile
@@ -10,6 +10,7 @@ ENV POLUS_LOG="INFO"
 WORKDIR ${EXEC_DIR}
 
 # Initialize ImageJ
+pip3 install pyimagej==1.4.1 jpype1==1.5.0 scyjava==1.9.1 imglyb==2.1.0
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
 # TODO: Change the tool_dir to the tool directory

diff --git a/formats/tabular-converter-tool/Dockerfile b/formats/tabular-converter-tool/Dockerfile
@@ -10,6 +10,7 @@ ENV POLUS_LOG="INFO"
 WORKDIR ${EXEC_DIR}
 
 # Initialize ImageJ
+pip3 install pyimagej==1.4.1 jpype1==1.5.0 scyjava==1.9.1 imglyb==2.1.0
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
 # TODO: Change the tool_dir to the tool directory

diff --git a/formats/tabular-to-arrow-tool/Dockerfile b/formats/tabular-to-arrow-tool/Dockerfile
@@ -10,6 +10,7 @@ ENV POLUS_LOG="INFO"
 WORKDIR ${EXEC_DIR}
 
 # Initialize ImageJ
+pip3 install pyimagej==1.4.1 jpype1==1.5.0 scyjava==1.9.1 imglyb==2.1.0
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
 # TODO: Change the tool_dir to the tool directory

diff --git a/formats/vector-to-label-tool/Dockerfile b/formats/vector-to-label-tool/Dockerfile
@@ -10,6 +10,7 @@ ENV POLUS_LOG="INFO"
 WORKDIR ${EXEC_DIR}
 
 # Initialize ImageJ
+pip3 install pyimagej==1.4.1 jpype1==1.5.0 scyjava==1.9.1 imglyb==2.1.0
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
 # TODO: Change the tool_dir to the tool directory

diff --git a/regression/basic-flatfield-estimation-tool/Dockerfile b/regression/basic-flatfield-estimation-tool/Dockerfile
@@ -40,6 +40,7 @@ ENV DATA_DIR="/data"
 WORKDIR ${EXEC_DIR}
 
 # Initialize ImageJ
+pip3 install pyimagej==1.4.1 jpype1==1.5.0 scyjava==1.9.1 imglyb==2.1.0
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
 # TODO: Change the tool_dir to the tool directory

diff --git a/regression/theia-bleedthrough-estimation-tool/Dockerfile b/regression/theia-bleedthrough-estimation-tool/Dockerfile
@@ -39,6 +39,7 @@ ENV DATA_DIR="/data"
 # Work directory defined in the base container
 WORKDIR ${EXEC_DIR}# Initialize ImageJ
 
+pip3 install pyimagej==1.4.1 jpype1==1.5.0 scyjava==1.9.1 imglyb==2.1.0
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
 # TODO: Change the tool_dir to the tool directory

diff --git a/segmentation/cell-border-segmentation-tool/Dockerfile b/segmentation/cell-border-segmentation-tool/Dockerfile
@@ -10,6 +10,7 @@ ENV POLUS_LOG="INFO"
 WORKDIR ${EXEC_DIR}
 
 # Initialize ImageJ
+pip3 install pyimagej==1.4.1 jpype1==1.5.0 scyjava==1.9.1 imglyb==2.1.0
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
 # TODO: Change the tool_dir to the tool directory

diff --git a/segmentation/mesmer-inference-tool/Dockerfile b/segmentation/mesmer-inference-tool/Dockerfile
@@ -23,6 +23,7 @@ RUN ln -sf /usr/bin/python3.9 /usr/bin/python3
 WORKDIR ${EXEC_DIR}
 
 # Initialize ImageJ
+pip3 install pyimagej==1.4.1 jpype1==1.5.0 scyjava==1.9.1 imglyb==2.1.0
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
 # TODO: Change the tool_dir to the tool directory

diff --git a/segmentation/mesmer-training-tool/Dockerfile b/segmentation/mesmer-training-tool/Dockerfile
@@ -23,6 +23,7 @@ RUN ln -sf /usr/bin/python3.9 /usr/bin/python3
 WORKDIR ${EXEC_DIR}
 
 # Initialize ImageJ
+pip3 install pyimagej==1.4.1 jpype1==1.5.0 scyjava==1.9.1 imglyb==2.1.0
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
 # TODO: Change the tool_dir to the tool directory

diff --git a/transforms/images/apply-flatfield-tool/Dockerfile b/transforms/images/apply-flatfield-tool/Dockerfile
@@ -10,6 +10,7 @@ ENV POLUS_LOG="INFO"
 WORKDIR ${EXEC_DIR}
 
 # Initialize ImageJ
+pip3 install pyimagej==1.4.1 jpype1==1.5.0 scyjava==1.9.1 imglyb==2.1.0
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
 # TODO: Change the tool_dir to the tool directory

diff --git a/transforms/images/binary-operations-tool/Dockerfile b/transforms/images/binary-operations-tool/Dockerfile
@@ -10,6 +10,7 @@ ENV POLUS_LOG="INFO"
 WORKDIR ${EXEC_DIR}
 
 # Initialize ImageJ
+pip3 install pyimagej==1.4.1 jpype1==1.5.0 scyjava==1.9.1 imglyb==2.1.0
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
 # TODO: Change the tool_dir to the tool directory

diff --git a/transforms/images/image-assembler-tool/Dockerfile b/transforms/images/image-assembler-tool/Dockerfile
@@ -10,6 +10,7 @@ ENV POLUS_LOG="INFO"
 WORKDIR ${EXEC_DIR}
 
 # Initialize ImageJ
+pip3 install pyimagej==1.4.1 jpype1==1.5.0 scyjava==1.9.1 imglyb==2.1.0
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
 # TODO: Change the tool_dir to the tool directory

diff --git a/transforms/images/image-calculator-tool/Dockerfile b/transforms/images/image-calculator-tool/Dockerfile
@@ -10,6 +10,7 @@ ENV POLUS_LOG="INFO"
 WORKDIR ${EXEC_DIR}
 
 # Initialize ImageJ
+pip3 install pyimagej==1.4.1 jpype1==1.5.0 scyjava==1.9.1 imglyb==2.1.0
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
 # TODO: Change the tool_dir to the tool directory

diff --git a/transforms/images/lumos-bleedthrough-correction-tool/Dockerfile b/transforms/images/lumos-bleedthrough-correction-tool/Dockerfile
@@ -10,6 +10,7 @@ ENV POLUS_LOG="INFO"
 WORKDIR ${EXEC_DIR}
 
 # Initialize ImageJ
+pip3 install pyimagej==1.4.1 jpype1==1.5.0 scyjava==1.9.1 imglyb==2.1.0
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
 # TODO: Change the tool_dir to the tool directory

diff --git a/transforms/images/montage-tool/Dockerfile b/transforms/images/montage-tool/Dockerfile
@@ -10,6 +10,7 @@ ENV POLUS_LOG="INFO"
 WORKDIR ${EXEC_DIR}
 
 # Initialize ImageJ
+pip3 install pyimagej==1.4.1 jpype1==1.5.0 scyjava==1.9.1 imglyb==2.1.0
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
 # TODO: Change the tool_dir to the tool directory

diff --git a/transforms/images/roi-relabel-tool/Dockerfile b/transforms/images/roi-relabel-tool/Dockerfile
@@ -10,6 +10,7 @@ ENV POLUS_LOG="INFO"
 WORKDIR ${EXEC_DIR}
 
 # Initialize ImageJ
+pip3 install pyimagej==1.4.1 jpype1==1.5.0 scyjava==1.9.1 imglyb==2.1.0
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
 # TODO: Change the tool_dir to the tool directory

diff --git a/transforms/tabular/tabular-thresholding-tool/Dockerfile b/transforms/tabular/tabular-thresholding-tool/Dockerfile
@@ -10,6 +10,7 @@ ENV POLUS_LOG="INFO"
 WORKDIR ${EXEC_DIR}
 
 # Initialize ImageJ
+pip3 install pyimagej==1.4.1 jpype1==1.5.0 scyjava==1.9.1 imglyb==2.1.0
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
 # TODO: Change the tool_dir to the tool directory

diff --git a/utils/rxiv-download-tool/Dockerfile b/utils/rxiv-download-tool/Dockerfile
@@ -10,6 +10,7 @@ ENV POLUS_LOG="INFO"
 WORKDIR ${EXEC_DIR}
 
 # Initialize ImageJ
+pip3 install pyimagej==1.4.1 jpype1==1.5.0 scyjava==1.9.1 imglyb==2.1.0
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
 # TODO: Change the tool_dir to the tool directory

diff --git a/visualization/microjson-to-ome-tool/Dockerfile b/visualization/microjson-to-ome-tool/Dockerfile
@@ -10,6 +10,7 @@ ENV POLUS_LOG="INFO"
 WORKDIR ${EXEC_DIR}
 
 # Initialize ImageJ
+pip3 install pyimagej==1.4.1 jpype1==1.5.0 scyjava==1.9.1 imglyb==2.1.0
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
 # TODO: Change the tool_dir to the tool directory

diff --git a/visualization/ome-to-microjson-tool/Dockerfile b/visualization/ome-to-microjson-tool/Dockerfile
@@ -10,6 +10,7 @@ ENV POLUS_LOG="INFO"
 WORKDIR ${EXEC_DIR}
 
 # Initialize ImageJ
+pip3 install pyimagej==1.4.1 jpype1==1.5.0 scyjava==1.9.1 imglyb==2.1.0
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
 # TODO: Change the tool_dir to the tool directory

diff --git a/visualization/precompute-slide-tool/Dockerfile b/visualization/precompute-slide-tool/Dockerfile
@@ -10,6 +10,7 @@ ENV POLUS_LOG="INFO"
 WORKDIR ${EXEC_DIR}
 
 # Initialize ImageJ
+pip3 install pyimagej==1.4.1 jpype1==1.5.0 scyjava==1.9.1 imglyb==2.1.0
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
 # TODO: Change the tool_dir to the tool directory

diff --git a/visualization/tabular-to-microjson-tool/Dockerfile b/visualization/tabular-to-microjson-tool/Dockerfile
@@ -10,6 +10,7 @@ ENV POLUS_LOG="INFO"
 WORKDIR ${EXEC_DIR}
 
 # Initialize ImageJ
+pip3 install pyimagej==1.4.1 jpype1==1.5.0 scyjava==1.9.1 imglyb==2.1.0
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
 # TODO: Change the tool_dir to the tool directory