add ability to pin bigstitcher version

- by manually downloading jar files
- this pins to an earlier version (hoping this will fix the black-bars
issue I am encountering.. )

Dockerfile

@@ -57,17 +57,19 @@ RUN mkdir /opt/fiji \
 ENV PATH $PATH:/opt/fiji/Fiji.app
 
 
-# Update URLs use https
-RUN ImageJ-linux64 --update edit-update-site ImageJ https://update.imagej.net/ \
- && ImageJ-linux64 --update edit-update-site Fiji https://update.fiji.sc/ \
- && ImageJ-linux64 --update edit-update-site Java-8 https://sites.imagej.net/Java-8/
+# add bigstitcher jars manually so we obtain a fixed version (note: need to handle dependencies manually in this case)
+COPY fiji_jars.txt /opt/fiji/fiji_jars.txt
+COPY fiji_plugins.txt /opt/fiji/fiji_plugins.txt
 
+# Loop over each URL in amd download each JAR
+RUN cat /opt/fiji/fiji_jars.txt | while read url; do \
+        wget "$url" --directory-prefix=/opt/fiji/Fiji.app/jars; \
+    done
+
+RUN cat /opt/fiji/fiji_plugins.txt | while read url; do \
+        wget "$url" --directory-prefix=/opt/fiji/Fiji.app/plugins; \
+    done
 
-#install bigstitcher
-RUN ImageJ-linux64 --update  add-update-site BigStitcher https://sites.imagej.net/BigStitcher/ \
- && ImageJ-linux64  --update refresh-update-sites \
- && ImageJ-linux64  --update  update \
- && ImageJ-linux64  --update  list 
 
 # Stage: itksnap (built with Ubuntu16.04 - glibc 2.23)
 FROM khanlab/itksnap:main as itksnap

README.md

@@ -1,3 +1,13 @@
 # SPIMprep_deps
 
 Container for SPIMprep dependencies (Fiji, bigstitcher, python)
+
+
+Note: There doesn't seem to be an easy way to pin the version of Fiji plugins (bigstitcher), and updating to the latest version might be breaking things.. 
+So we define fiji plugins and dependencies manually, by providing lists of urls for each.
+
+The URLs were determined by going to the bigstitcher maven page (of the version to install), e.g.:
+https://mvnrepository.com/artifact/net.preibisch/BigStitcher/1.2.10
+
+Then going through the list of dependencies and grabbing the URLs for jar files. The dependency jars are added to `fiji_jars.txt`. and the plugin jars are added to `fiji_plugins.txt`. The Dockerfile downloads them and puts them in the fiji jars and plugins folder respectively. 
+

fiji_jars.txt

@@ -0,0 +1,17 @@
+https://maven.scijava.org/content/repositories/public/net/preibisch/multiview-reconstruction/3.2.3/multiview-reconstruction-3.2.3.jar
+https://maven.imagej.net/content/repositories/releases/sc/fiji/spim_data/2.2.7/spim_data-2.2.7.jar
+https://maven.scijava.org/content/repositories/releases/sc/fiji/bigdataviewer-core/10.4.10/bigdataviewer-core-10.4.10.jar
+https://maven.scijava.org/content/repositories/releases/sc/fiji/bigdataviewer-vistools/1.0.0-beta-32/bigdataviewer-vistools-1.0.0-beta-32.jar
+https://repo1.maven.org/maven2/net/imglib2/imglib2/6.2.0/imglib2-6.2.0.jar
+https://maven.imagej.net/content/repositories/public/net/imglib2/imglib2-cache/1.0.0-beta-17/imglib2-cache-1.0.0-beta-17.jar
+http://dev.loci.wisc.edu/maven2/releases/net/preibisch/multiview-simulation/0.2.0/multiview-simulation-0.2.0.jar
+http://dev.loci.wisc.edu/maven2/releases/mpicbg/mpicbg/1.5.0/mpicbg-1.5.0.jar
+https://repo1.maven.org/maven2/gov/nist/math/jama/1.0.3/jama-1.0.3.jar
+https://repo1.maven.org/maven2/com/google/guava/guava/31.1-jre/guava-31.1-jre.jar
+https://maven.scijava.org/content/repositories/releases/net/imglib2/imglib2-algorithm/0.14.0/imglib2-algorithm-0.14.0.jar
+https://maven.scijava.org/content/repositories/public/net/imglib2/imglib2-realtransform/4.0.1/imglib2-realtransform-4.0.1.jar
+https://maven.scijava.org/content/repositories/public/sc/fiji/fiji-lib/2.1.3/fiji-lib-2.1.3.jar
+https://maven.imagej.net/content/repositories/releases/net/imglib2/imglib2-algorithm-fft/0.2.1/imglib2-algorithm-fft-0.2.1.jar
+https://repo1.maven.org/maven2/net/imagej/ij/1.54f/ij-1.54f.jar
+https://maven.scijava.org/content/repositories/releases/net/imglib2/imglib2-ij/2.0.1/imglib2-ij-2.0.1.jar
+

fiji_plugins.txt

@@ -0,0 +1 @@
+https://maven.scijava.org/content/repositories/releases/net/preibisch/BigStitcher/1.2.10/BigStitcher-1.2.10.jar