diff --git a/437_Fiji/Fiji-2.14.0-Java-11.eb b/437_Fiji/Fiji-2.14.0-Java-11.eb new file mode 100644 index 00000000..0748b9fb --- /dev/null +++ b/437_Fiji/Fiji-2.14.0-Java-11.eb @@ -0,0 +1,58 @@ +easyblock = 'PackedBinary' + +name = 'Fiji' +version = '2.14.0' +versionsuffix = '-Java-%(javaver)s' + +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 = ['%(namelower)s-%(version)s-nojre.zip'] +checksums = ['1dcf6efd7a2c99b70ab921bea3b9e7c74ef99acf35b9857199de7f9c424187db'] + +dependencies = [('Java', '11', '', 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/', + # 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', +] + +sanity_check_paths = { + 'files': ['ImageJ-linux64'], + 'dirs': [], +} + +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 +""" + +moduleclass = 'vis' + +# TODO +# == 2024-11-20 13:15:33,677 build_log.py:171 ERROR EasyBuild crashed with an error (at easybuild/easybuild-framework/easybuild/base/exceptions.py:126 in __init__): cmd "/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/Fiji/2.14.0-Java-11/ImageJ-linux64 --headless --update edit-update-site "ImageScience" https://sites.imagej.net/ImageScience/" exited with exit code 1 and output: +# Could not load Java library '/kyukon/home/apps/RHEL8/cascadelake-ib/software/Java/11.0.20/lib/amd64/server/libjvm.so': /kyukon/home/apps/RHEL8/cascadelake-ib/software/Java/11.0.20/lib/amd64/server/libjvm.so: cannot open shared object file: No such file or directory +# Warning: falling back to System JVM +# Unrecognized option: -Xincgc +# Error: Could not create the Java Virtual Machine. +# Error: A fatal exception has occurred. Program will exit. +# (at easybuild/easybuild-framework/easybuild/tools/run.py:695 in parse_cmd_output) diff --git a/437_Fiji/Fiji-2.16.0-Java-11.eb b/437_Fiji/Fiji-2.16.0-Java-11.eb new file mode 100644 index 00000000..081a1a45 --- /dev/null +++ b/437_Fiji/Fiji-2.16.0-Java-11.eb @@ -0,0 +1,59 @@ +easyblock = 'PackedBinary' + +name = 'Fiji' +version = '2.16.0' +local_version = '20241022' +versionsuffix = '-Java-%(javaver)s' + +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/future/'] +sources = ['%%(namelower)s-future-linux64-%s.zip' % local_version] +checksums = ['9501837d1e5d8bf0549fa32cf157a48ab312d2470d9da0f82b330601ac7f5956'] + +dependencies = [('Java', '11', '', 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/', +# # 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 --help', +# '%(installdir)s/ImageJ-linux64 --headless --update update', +# '%(installdir)s/ImageJ-linux64 --headless --update', +# ] + +sanity_check_paths = { + # 'files': ['ImageJ-linux64'], + 'files': ['fiji-linux-x64'], + 'dirs': [], +} + +sanity_check_commands = ['fiji-linux-x64'] + +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 +""" + +moduleclass = 'vis' + +# TODO +# == 2024-11-20 13:51:23,376 build_log.py:171 ERROR EasyBuild crashed with an error (at easybuild/easybuild-framework/easybuild/base/exceptions.py:126 in __init__): Sanity check failed: sanity check command fiji-linux-x64 --help exited with code 1 (output: fiji-linux-x64: /lib64/libc.so.6: version `GLIBC_2.34' not found (required by fiji-linux-x64) +# ) (at easybuild/easybuild-framework/easybuild/framework/easyblock.py:3670 in _sanity_check_step)