Merge pull request #18 from CGDogan/biof

Bioformats

.gitignore

@@ -80,3 +80,6 @@ Makefile.in
 /ltmain.sh
 /m4/
 /missing
+
+# BioFormats either copied by Docker of copied manually and locally
+BFBridge/

Dockerfile

@@ -28,6 +28,9 @@ RUN ln -s /etc/apache2/mods-available/proxy.conf /etc/apache2/mods-enabled/proxy
 COPY apache2.conf /etc/apache2/apache2.conf
 COPY ports.conf /etc/apache2/ports.conf
 
+## Print BioFormats errors, etc. to Docker console (stderr)
+#RUN ln -sf /proc/self/fd/1 /var/log/apache2/error.log
+
 ###  iipsrv
 WORKDIR /root/src/iipsrv
 RUN ./autogen.sh

README.md

@@ -3,6 +3,8 @@ Containerized IIP
 
 ## building and running
 
+Unless using caMicroscope Distro Docker, [BFBridge](https://github.com/camicroscope/BFBridge) needs to be cloned and placed next to iipsrv/, so that this project's root iipimage/ has subfolders iipimage/ and BFBridge/
+
 docker build . -t iipsrv
 
 docker run iipsrv -d -p 4010:80

apache2-iipsrv-fcgid.conf

@@ -27,6 +27,8 @@ FcgidInitialEnv MAX_CVT "5000"
 #FcgidInitialEnv FILESYSTEM_PREFIX "/mnt/images/"
 FcgidInitialEnv LD_LIBRARY_PATH "/usr/local/lib"
 FcgidInitialEnv MAX_TILE_CACHE_SIZE "64"
+FcgidInitialEnv BFBRIDGE_CACHEDIR "/tmp/"
+FcgidInitialEnv BFBRIDGE_CLASSPATH "/usr/lib/java"
 
 # Define the idle timeout as unlimited and the number of
 # processes we want

fcgid.conf

@@ -27,6 +27,8 @@ FcgidInitialEnv MAX_CVT "5000"
 FcgidInitialEnv LD_LIBRARY_PATH "/usr/local/lib"
 FcgidInitialEnv MAX_TILE_CACHE_SIZE "64"
 FcgidInitialEnv CORS "*"
+FcgidInitialEnv BFBRIDGE_CACHEDIR "/tmp/"
+FcgidInitialEnv BFBRIDGE_CLASSPATH "/usr/lib/java"
 
 # Define the idle timeout as unlimited and the number of
 # processes we want

iip_httpd.conf

@@ -28,5 +28,7 @@ FastCgiServer /var/www/localhost/fcgi-bin/iipsrv.fcgi \
 -initial-env JPEG_QUALITY=50 \
 -initial-env MAX_CVT=3000 \
 -initial-env CORS=* \
+-initial-env BFBRIDGE_CACHEDIR=/tmp/ \
+-initial-env BFBRIDGE_CLASSPATH=/usr/lib/java \
 -listen-queue-depth 2048 \
 -processes 1