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Fiji archive file changed to .zip #22260

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51 changes: 51 additions & 0 deletions easybuild/easyconfigs/f/Fiji/Fiji-20240605-1417.eb
Original file line number Diff line number Diff line change
@@ -0,0 +1,51 @@
easyblock = 'PackedBinary'

name = 'Fiji'
version = '20240605-1417'
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I think we should using this. Their github do tag releases:
https://github.com/fiji/fiji/tags
https://github.com/fiji/fiji/archive/refs/tags/fiji-2.16.0.tar.gz

so they do have actual version numbers


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/%(namelower)s/archive/%(version)s']
sources = [{
'download_filename': '%(namelower)s-nojre.zip',
'filename': '%(namelower)s-nojre-%(version)s.zip',
}]
checksums = ['d9329f79f548db1d74143146215b02f18a005549e57847cf8df3bedb2905ab12']

dependencies = [('Java', '1.8', '', SYSTEM)]
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1.8 is the old Oracle java, please avoid using it. Based on earlier PRs, at least JAva 11 should work for this software. So, maybe 11 or 17?


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'