diff --git a/easybuild/easyconfigs/f/Fiji/Fiji-2.14.0-Java-8.eb b/easybuild/easyconfigs/f/Fiji/Fiji-2.14.0-Java-8.eb new file mode 100644 index 00000000000..4cf9eca7af8 --- /dev/null +++ b/easybuild/easyconfigs/f/Fiji/Fiji-2.14.0-Java-8.eb @@ -0,0 +1,54 @@ +# 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 = '2.14.0' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://fiji.sc/' +description = """Fiji is an image processing packageā€”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', '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 --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 --default-gc --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 +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'