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{vis}[system/system] Fiji v2.14.0 w/ Java 8 #22196

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{vis}[system/system] Fiji v2.14.0 w/ Java 8 #22196

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@sassy-crick sassy-crick commented Jan 22, 2025 •
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(created using eb --new-pr)
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This PR is using the latest Java-8 version as Fiji is still tied to Java-8, at least for now.
See here for more information

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Updated software Fiji-2.14.0-Java-8.eb

Diff against Fiji-2.14.0-Java-11.eb

easybuild/easyconfigs/f/Fiji/Fiji-2.14.0-Java-11.eb

diff --git a/easybuild/easyconfigs/f/Fiji/Fiji-2.14.0-Java-11.eb b/easybuild/easyconfigs/f/Fiji/Fiji-2.14.0-Java-8.eb
index 6e3f4cddae..4cf9eca7af 100644
--- a/easybuild/easyconfigs/f/Fiji/Fiji-2.14.0-Java-11.eb
+++ b/easybuild/easyconfigs/f/Fiji/Fiji-2.14.0-Java-8.eb
@@ -1,3 +1,6 @@
+# Changed to Java-8 to avoid errors until Fiji can user newer Java Versions
+# Author: J. Sassmannshausen (Imperial College London/UK)
+
 easyblock = 'PackedBinary'
 
 name = 'Fiji'
@@ -15,24 +18,24 @@ source_urls = ['https://downloads.imagej.net/fiji/releases/%(version)s']
 sources = ['%(namelower)s-%(version)s-nojre.zip']
 checksums = ['1dcf6efd7a2c99b70ab921bea3b9e7c74ef99acf35b9857199de7f9c424187db']
 
-dependencies = [('Java', '11', '', SYSTEM)]
+dependencies = [('Java', '8', '', SYSTEM)]
 
 postinstallcmds = [
     # Remove binaries for other platforms
     'rm %(installdir)s/{ImageJ-win32.exe,ImageJ-win64.exe}',
     # Enable any update site (edit existing site with same parameters to enable it)
     # Full list at https://imagej.github.io/list-of-update-sites/
-    '%(installdir)s/ImageJ-linux64 --default-gc --java-home "$EBROOTJAVA/lib/server/" --headless'
+    '%(installdir)s/ImageJ-linux64 --default-gc --headless'
     ' --update edit-update-site "ImageScience" https://sites.imagej.net/ImageScience/',
-    '%(installdir)s/ImageJ-linux64 --default-gc --java-home "$EBROOTJAVA/lib/server/" --headless'
+    '%(installdir)s/ImageJ-linux64 --default-gc --headless'
     ' --update edit-update-site "3D ImageJ Suite" https://sites.imagej.net/Tboudier/',
-    '%(installdir)s/ImageJ-linux64 --default-gc --java-home "$EBROOTJAVA/lib/server/" --headless'
+    '%(installdir)s/ImageJ-linux64 --default-gc --headless'
     ' --update edit-update-site "ilastik" https://sites.imagej.net/Ilastik/',
     # Add a new update site
     # '%(installdir)s/ImageJ-linux64 --headless --update add-update-site "New Name"'
     # ' https://site.url/NewName/',
     # Update the installation
-    '%(installdir)s/ImageJ-linux64 --default-gc --java-home "$EBROOTJAVA/lib/server/" --headless --update update',
+    '%(installdir)s/ImageJ-linux64 --default-gc --headless --update update',
 ]
 
 sanity_check_paths = {
@@ -44,9 +47,8 @@ modloadmsg = """
 Additional plugins can be installed in your $HOME/.plugins folder or requested to user support
 Use ImageJ/Fiji in headless mode in your scripts with the command `ImageJ-linux64 --headless`
 More information at https://imagej.net/Headless
-Also for Fiji 2.14.0 the arguments `--default-gc --java-home "$EBROOTJAVA/lib/server/"`
-should always be used when running `ImageJ-linux64` commands to avoid errors like:
-`Could not load Java library` and `Unrecognized option: -Xincgc`.
+Also for Fiji 2.14.0 the arguments `--default-gc` should always be used when running
+`ImageJ-linux64` commands to avoid error messages
 """
 
 moduleclass = 'vis'
Diff against Fiji-2.9.0-Java-8.eb

easybuild/easyconfigs/f/Fiji/Fiji-2.9.0-Java-8.eb

diff --git a/easybuild/easyconfigs/f/Fiji/Fiji-2.9.0-Java-8.eb b/easybuild/easyconfigs/f/Fiji/Fiji-2.14.0-Java-8.eb
index a025352372..4cf9eca7af 100644
--- a/easybuild/easyconfigs/f/Fiji/Fiji-2.9.0-Java-8.eb
+++ b/easybuild/easyconfigs/f/Fiji/Fiji-2.14.0-Java-8.eb
@@ -1,19 +1,22 @@
+# Changed to Java-8 to avoid errors until Fiji can user newer Java Versions
+# Author: J. Sassmannshausen (Imperial College London/UK)
+
 easyblock = 'PackedBinary'
 
 name = 'Fiji'
-version = '2.9.0'
+version = '2.14.0'
 versionsuffix = '-Java-%(javaver)s'
 
-homepage = 'https://fiji.sc'
+homepage = 'https://fiji.sc/'
 description = """Fiji is an image processing package—a 'batteries-included' distribution of
  ImageJ, bundling a lot of plugins which facilitate scientific image analysis.
 This release is based on ImageJ-2.1.0 and Fiji-2.1.1"""
 
 toolchain = SYSTEM
 
-source_urls = ['https://downloads.imagej.net/fiji/releases/%(version)s/']
-sources = ['fiji-%(version)s-nojre.zip']
-checksums = ['970fb80cf2a4fe8bfcecc2cc9a8617b9ab28f19fbe229ea6ae2f7f42674c8a42']
+source_urls = ['https://downloads.imagej.net/fiji/releases/%(version)s']
+sources = ['%(namelower)s-%(version)s-nojre.zip']
+checksums = ['1dcf6efd7a2c99b70ab921bea3b9e7c74ef99acf35b9857199de7f9c424187db']
 
 dependencies = [('Java', '8', '', SYSTEM)]
 
@@ -22,17 +25,17 @@ postinstallcmds = [
     'rm %(installdir)s/{ImageJ-win32.exe,ImageJ-win64.exe}',
     # Enable any update site (edit existing site with same parameters to enable it)
     # Full list at https://imagej.github.io/list-of-update-sites/
-    '%(installdir)s/ImageJ-linux64 --headless --update edit-update-site "ImageScience"'
-    ' https://sites.imagej.net/ImageScience/',
-    '%(installdir)s/ImageJ-linux64 --headless --update edit-update-site "3D ImageJ Suite"'
-    ' https://sites.imagej.net/Tboudier/',
-    '%(installdir)s/ImageJ-linux64 --headless --update edit-update-site "ilastik"'
-    ' https://sites.imagej.net/Ilastik/',
+    '%(installdir)s/ImageJ-linux64 --default-gc --headless'
+    ' --update edit-update-site "ImageScience" https://sites.imagej.net/ImageScience/',
+    '%(installdir)s/ImageJ-linux64 --default-gc --headless'
+    ' --update edit-update-site "3D ImageJ Suite" https://sites.imagej.net/Tboudier/',
+    '%(installdir)s/ImageJ-linux64 --default-gc --headless'
+    ' --update edit-update-site "ilastik" https://sites.imagej.net/Ilastik/',
     # Add a new update site
     # '%(installdir)s/ImageJ-linux64 --headless --update add-update-site "New Name"'
     # ' https://site.url/NewName/',
     # Update the installation
-    '%(installdir)s/ImageJ-linux64 --headless --update update',
+    '%(installdir)s/ImageJ-linux64 --default-gc --headless --update update',
 ]
 
 sanity_check_paths = {
@@ -44,6 +47,8 @@ modloadmsg = """
 Additional plugins can be installed in your $HOME/.plugins folder or requested to user support
 Use ImageJ/Fiji in headless mode in your scripts with the command `ImageJ-linux64 --headless`
 More information at https://imagej.net/Headless
+Also for Fiji 2.14.0 the arguments `--default-gc` should always be used when running
+`ImageJ-linux64` commands to avoid error messages
 """
 
 moduleclass = 'vis'
Diff against Fiji-2.9.0-Java-1.8.eb

easybuild/easyconfigs/f/Fiji/Fiji-2.9.0-Java-1.8.eb

diff --git a/easybuild/easyconfigs/f/Fiji/Fiji-2.9.0-Java-1.8.eb b/easybuild/easyconfigs/f/Fiji/Fiji-2.14.0-Java-8.eb
index c655cd1654..4cf9eca7af 100644
--- a/easybuild/easyconfigs/f/Fiji/Fiji-2.9.0-Java-1.8.eb
+++ b/easybuild/easyconfigs/f/Fiji/Fiji-2.14.0-Java-8.eb
@@ -1,38 +1,41 @@
+# Changed to Java-8 to avoid errors until Fiji can user newer Java Versions
+# Author: J. Sassmannshausen (Imperial College London/UK)
+
 easyblock = 'PackedBinary'
 
 name = 'Fiji'
-version = '2.9.0'
+version = '2.14.0'
 versionsuffix = '-Java-%(javaver)s'
 
-homepage = 'https://fiji.sc'
+homepage = 'https://fiji.sc/'
 description = """Fiji is an image processing package—a 'batteries-included' distribution of
  ImageJ, bundling a lot of plugins which facilitate scientific image analysis.
 This release is based on ImageJ-2.1.0 and Fiji-2.1.1"""
 
 toolchain = SYSTEM
 
-source_urls = ['https://downloads.imagej.net/fiji/releases/%(version)s/']
-sources = ['fiji-%(version)s-nojre.zip']
-checksums = ['970fb80cf2a4fe8bfcecc2cc9a8617b9ab28f19fbe229ea6ae2f7f42674c8a42']
+source_urls = ['https://downloads.imagej.net/fiji/releases/%(version)s']
+sources = ['%(namelower)s-%(version)s-nojre.zip']
+checksums = ['1dcf6efd7a2c99b70ab921bea3b9e7c74ef99acf35b9857199de7f9c424187db']
 
-dependencies = [('Java', '1.8', '', SYSTEM)]
+dependencies = [('Java', '8', '', SYSTEM)]
 
 postinstallcmds = [
     # Remove binaries for other platforms
     'rm %(installdir)s/{ImageJ-win32.exe,ImageJ-win64.exe}',
     # Enable any update site (edit existing site with same parameters to enable it)
     # Full list at https://imagej.github.io/list-of-update-sites/
-    '%(installdir)s/ImageJ-linux64 --headless --update edit-update-site "ImageScience"'
-    ' https://sites.imagej.net/ImageScience/',
-    '%(installdir)s/ImageJ-linux64 --headless --update edit-update-site "3D ImageJ Suite"'
-    ' https://sites.imagej.net/Tboudier/',
-    '%(installdir)s/ImageJ-linux64 --headless --update edit-update-site "ilastik"'
-    ' https://sites.imagej.net/Ilastik/',
+    '%(installdir)s/ImageJ-linux64 --default-gc --headless'
+    ' --update edit-update-site "ImageScience" https://sites.imagej.net/ImageScience/',
+    '%(installdir)s/ImageJ-linux64 --default-gc --headless'
+    ' --update edit-update-site "3D ImageJ Suite" https://sites.imagej.net/Tboudier/',
+    '%(installdir)s/ImageJ-linux64 --default-gc --headless'
+    ' --update edit-update-site "ilastik" https://sites.imagej.net/Ilastik/',
     # Add a new update site
     # '%(installdir)s/ImageJ-linux64 --headless --update add-update-site "New Name"'
     # ' https://site.url/NewName/',
     # Update the installation
-    '%(installdir)s/ImageJ-linux64 --headless --update update',
+    '%(installdir)s/ImageJ-linux64 --default-gc --headless --update update',
 ]
 
 sanity_check_paths = {
@@ -44,6 +47,8 @@ modloadmsg = """
 Additional plugins can be installed in your $HOME/.plugins folder or requested to user support
 Use ImageJ/Fiji in headless mode in your scripts with the command `ImageJ-linux64 --headless`
 More information at https://imagej.net/Headless
+Also for Fiji 2.14.0 the arguments `--default-gc` should always be used when running
+`ImageJ-linux64` commands to avoid error messages
 """
 
 moduleclass = 'vis'

@smoors
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smoors commented Jan 23, 2025

This PR is using the latest Java-8 version as Fiji is still tied to Java-8, at least for now.

shouldn't we remove Fiji-2.14.0-Java-11.eb then?

@sassy-crick
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This PR is using the latest Java-8 version as Fiji is still tied to Java-8, at least for now.

shouldn't we remove Fiji-2.14.0-Java-11.eb then?

Good question. I am not the expert on Fiji but I am half-inclined to say yes, given the problems one of our user had. I find both solutions a bit half baked:

  • either you are using Java-8 with all the security issues which might be around it
    or
  • use Java-11 and all the problems it comes with it.
    The proper solution would be for Fiji to release a version build against a more modern Java in my opinion.
    We had an internal discussion and settled on the Java-8 solution.

@boegel what is your take here?

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@sassy-crick @smoors