From abc8d4d19a9172cf85d3a9d9a0b1041cb08a8c4b Mon Sep 17 00:00:00 2001
From: Ali Khan <alik@robarts.ca>
Date: Wed, 18 Sep 2024 20:50:00 -0400
Subject: [PATCH] update jars list (dead links), and strip after .jar

---
 Dockerfile    | 14 ++++++++------
 fiji_jars.txt |  5 ++---
 2 files changed, 10 insertions(+), 9 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 226e8f1..e79b604 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -36,15 +36,15 @@ ENV JAVA_HOME=/usr/lib/jvm/java-1.8.0-amazon-corretto
 
 
 #install maven hdf5-tools deps, 7zip (for zarr zipstore archiving)
-RUN apt-get update && apt-get install -y maven hdf5-tools libblosc-dev p7zip-full && mkdir -p /opt/bin
+#RUN apt-get update && apt-get install -y maven hdf5-tools libblosc-dev p7zip-full && mkdir -p /opt/bin
 
-ENV PATH $PATH:/opt/bin
+#ENV PATH $PATH:/opt/bin
 
 #install n5-utils
-RUN cd /opt && git clone https://github.com/saalfeldlab/n5-utils && cd n5-utils && ./install /opt/bin
+#RUN cd /opt && git clone https://github.com/saalfeldlab/n5-utils && cd n5-utils && ./install /opt/bin
 
 #install bigstitcher-spark, and customize launcher to include args for mem and cpu 
-RUN cd /opt && git clone https://github.com/akhanf/BigStitcher-Spark.git && cd BigStitcher-Spark && ./install -t 32 -m 128 && cp -v affine-fusion /opt/bin && cp -v target/BigStitcher-Spark-0.0.2-SNAPSHOT.jar /opt/bin 
+#RUN cd /opt && git clone https://github.com/akhanf/BigStitcher-Spark.git && cd BigStitcher-Spark && ./install -t 32 -m 128 && cp -v affine-fusion /opt/bin && cp -v target/BigStitcher-Spark-0.0.2-SNAPSHOT.jar /opt/bin 
 
 # Install Fiji.
 RUN mkdir /opt/fiji \
@@ -63,11 +63,13 @@ 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 "$url" --directory-prefix=/opt/fiji/Fiji.app/jars; \
+        filename=$(basename "$url" | sed 's/\(\.jar\).*/\1/'); \
+        wget "$url" -O /opt/fiji/Fiji.app/jars/${filename}; \
     done
 
 RUN cat /opt/fiji/fiji_plugins.txt | while read url; do \
-        wget "$url" --directory-prefix=/opt/fiji/Fiji.app/plugins; \
+        filename=$(basename "$url" | sed 's/\(\.jar\).*/\1/'); \
+        wget "$url" -O /opt/fiji/Fiji.app/plugins/${filename}; \
     done
 
 
diff --git a/fiji_jars.txt b/fiji_jars.txt
index bfaf96f..8dfe52b 100644
--- a/fiji_jars.txt
+++ b/fiji_jars.txt
@@ -4,8 +4,8 @@ https://maven.scijava.org/content/repositories/releases/sc/fiji/bigdataviewer-co
 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://sites.imagej.net/BigStitcher/jars/multiview-simulation-0.2.0.jar-20180528174209
+https://downloads.micron.ox.ac.uk/fiji_update/mirrors/java-8/jars/mpicbg-1.5.0.jar-20230710192037
 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
@@ -14,4 +14,3 @@ https://maven.scijava.org/content/repositories/public/sc/fiji/fiji-lib/2.1.3/fij
 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
-