Initial Commit

Dockerfile

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+FROM python:3.6.9-stretch
+
+# ---------------------------------------------------------------------------------------------------------------------
+# Install Java, needed for Metric TreTrc using DIADEM.jar
+RUN apt-get update && apt-get install openjdk-8-jdk -y && apt-get clean
+
+# ---------------------------------------------------------------------------------------------------------------------
+# Install Cytomine python client (annotation exporter, compute metrics, helpers,...)
+RUN git clone https://github.com/cytomine-uliege/Cytomine-python-client.git && \
+    cd /Cytomine-python-client && git checkout tags/v2.3.0.poc.1 && pip install . && \
+    rm -r /Cytomine-python-client
+
+# ---------------------------------------------------------------------------------------------------------------------
+# Install Neubias-W5-Utilities (annotation exporter, compute metrics, helpers,...)    
+# It will get DiademMetric.jar and JSAP-2.1.jar files to compute DIADEM metric
+RUN apt-get update && apt-get install libgeos-dev -y && apt-get clean
+RUN git clone https://github.com/Neubias-WG5/neubiaswg5-utilities.git && \
+    cd /neubiaswg5-utilities/ && git checkout tags/v0.8.2 && pip install .
+
+# install utilities binaries
+RUN chmod +x /neubiaswg5-utilities/bin/*
+RUN cp /neubiaswg5-utilities/bin/* /usr/bin/
+
+# cleaning
+RUN rm -r /neubiaswg5-utilities    
+
+
+# --------------------------------------------------------------------------------------------
+# install required packages and download vaa3d
+RUN wget https://github.com/Vaa3D/release/releases/download/v3.458/Vaa3D_CentOS_64bit_v3.458.tar.gz --directory-prefix=/
+RUN tar -xvzf Vaa3D_CentOS_64bit_v3.458.tar.gz
+RUN apt-get update
+RUN apt-get install -y \
+        libqt4-svg \
+        libqt4-opengl \
+        libqt4-network \
+        libglu1-mesa
+RUN apt-get install -y curl xvfb libx11-dev libxtst-dev libxrender-dev
+
+# --------------------------------------------------------------------------------------------
+# Install scripts and models
+ADD wrapper.py /app/wrapper.py
+ADD workflow.py /app/workflow.py
+ADD swc_to_tiff_stack.py /app/swc_to_tiff_stack.py
+ADD descriptor.json /app/descriptor.json
+
+ENTRYPOINT ["python", "/app/wrapper.py"]
+
+

README.md

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+# W_Neuron3dTree_vaa3d_most
+Vaa3d MOST Vessel Tracer (MOST) dockerised workflow for BIAFLOWS
+
+### Full Description :
+ See on the [Bioimage Informatics Search Engine (BISE)](https://biii.eu) in the [most-raytracer](http://biii.eu/most-raytracer) section or in the [github repository](https://github.com/Vaa3D/vaa3d_tools/tree/master/released_plugins/v3d_plugins/neurontracing_MOST)
+
+### Publication:
+Link : http://www.sciencedirect.com/science/article/pii/S1053811913010598

descriptor.json

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+{
+    "name": "W_Neuron3dTree_vaa3d_most",
+    "container-image": {
+        "image": "neubiaswg5/w_neuron3dtree_vaa3d_most",
+        "type": "singularity"
+    },
+    "schema-version": "cytomine-0.1",
+    "description": "trace 3d tree with vaa3d MOST Vessel Tracer algorithm",
+    "command-line": "python wrapper.py CYTOMINE_HOST CYTOMINE_PUBLIC_KEY CYTOMINE_PRIVATE_KEY CYTOMINE_ID_PROJECT CYTOMINE_ID_SOFTWARE THRESHOLD SEED SLIP",
+    "inputs": [
+        {
+            "id": "cytomine_host",
+            "value-key": "@ID",
+            "command-line-flag": "--@id",
+            "name": "Cytomine host",
+            "description": "Cytomine server hostname",
+            "type": "String",
+            "optional": false,
+            "set-by-server": true
+        },
+        {
+            "id": "cytomine_public_key",
+            "value-key": "@ID",
+            "command-line-flag": "--@id",
+            "name": "Cytomine public key",
+            "description": "Cytomine public key",
+            "type": "String",
+            "optional": false,
+            "set-by-server": true
+        },
+        {
+            "id": "cytomine_private_key",
+            "value-key": "@ID",
+            "command-line-flag": "--@id",
+            "name": "Cytomine private key",
+            "description": "Cytomine private key",      
+            "type": "String",
+            "optional": false,
+            "set-by-server": true
+        },
+        {
+            "id": "cytomine_id_project",
+            "value-key": "@ID",
+            "command-line-flag": "--@id",
+            "name": "Cytomine project id",
+            "description": "Cytomine project id",
+            "type": "String",
+            "optional": false,
+            "set-by-server": true
+        },
+        {
+            "id": "cytomine_id_software",
+            "value-key": "@ID",
+            "command-line-flag": "--@id",
+            "name": "Cytomine software id",
+            "description": "Cytomine software id",
+            "type": "String",
+            "optional": false,
+            "set-by-server": true
+        },
+        {
+          "default-value": 20,
+          "name": "threshold",
+          "description": "the threshold value, default 20",
+          "set-by-server": false,
+          "value-key": "@ID",
+          "optional": true,
+          "id": "threshold",
+          "type": "Number",
+          "command-line-flag": "--@id"
+        },
+        {
+          "default-value": 20,
+          "name": "seed",
+          "description": "window size of the seed, default 20",
+          "set-by-server": false,
+          "value-key": "@ID",
+          "optional": true,
+          "id": "seed",
+          "type": "Number",
+          "command-line-flag": "--@id"
+        },
+        {
+          "default-value": 20,
+          "name": "slip",
+          "description": "window size to slip from seed, default 20",
+          "set-by-server": false,
+          "value-key": "@ID",
+          "optional": true,
+          "id": "slip",
+          "type": "Number",
+          "command-line-flag": "--@id"
+        }
+    ]
+}