From e21f2daa38c189fdc65c5e3265a26ba08c44e6bf Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 19 Jan 2024 15:56:20 +0000 Subject: [PATCH 1/3] adding easyconfigs: AFNI-24.0.01-foss-2023a.eb --- .../a/AFNI/AFNI-24.0.01-foss-2023a.eb | 68 +++++++++++++++++++ 1 file changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/a/AFNI/AFNI-24.0.01-foss-2023a.eb diff --git a/easybuild/easyconfigs/a/AFNI/AFNI-24.0.01-foss-2023a.eb b/easybuild/easyconfigs/a/AFNI/AFNI-24.0.01-foss-2023a.eb new file mode 100644 index 00000000000..7926d97d997 --- /dev/null +++ b/easybuild/easyconfigs/a/AFNI/AFNI-24.0.01-foss-2023a.eb @@ -0,0 +1,68 @@ +# Updated to use CMake and better installation routines +# Updated to version 24.0.01 +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'AFNI' +version = '24.0.01' + +homepage = 'http://afni.nimh.nih.gov/' +description = """AFNI is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - + a technique for mapping human brain activity.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'openmp': True, 'pic': True} + +source_urls = ['https://github.com/afni/afni/archive/'] +sources = ['AFNI_%(version)s.tar.gz'] +checksums = ['eb4135978bdf54be0ce1577b87c82ffe4ea4dfdeec21aa3a38e4a6929c9567b0'] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +dependencies = [ + ('tcsh', '6.24.10'), + ('Python', '3.11.3'), + ('X11', '20230603'), + ('motif', '2.3.8'), + ('R', '4.3.2'), + ('PyQt5', '5.15.10'), + ('expat', '2.5.0'), + ('libpng', '1.6.39'), + ('libjpeg-turbo', '2.1.5.1'), + ('GSL', '2.7'), + ('GLib', '2.77.1'), # must match version used in Qt5 (via PyQt5) + ('zlib', '1.2.13'), + ('freeglut', '3.4.0'), + ('Pillow', '10.0.0'), + ('matplotlib', '3.7.2'), + ('SciPy-bundle', '2023.07'), + ('Xvfb', '21.1.8'), + ('FFmpeg', '6.0'), # required for running the program +] + +# Make sure stuff does not get installed in .local +configopts = '-DSTANDARD_PYTHON_INSTALL=OFF ' + +# Changing permissions of some files +postinstallcmds = ['chmod a+x %(installdir)s/bin/afni_system_check.py ;'] +postinstallcmds += ['chmod a+x %(installdir)s/bin/uber_subject.py ; '] +postinstallcmds += ['chmod a+x %(installdir)s/bin/init_user_dotfiles.py ; '] +# Copying apparently missing files over +postinstallcmds += ['cp -f %(start_dir)s/src/discoraj/ClusterExplorer/ClustExp_HistTable.py %(installdir)s/bin ; '] +postinstallcmds += ['cp -f %(start_dir)s/src/discoraj/ClusterExplorer/ClustExp_StatParse.py %(installdir)s/bin ; '] +postinstallcmds += ['cp -rf %(start_dir)s/src/scripts_for_r %(installdir)s/bin ; '] +postinstallcmds += ['cp -rf %(start_dir)s/src/R_scripts %(installdir)s/bin/scripts_for_r ; '] + +sanity_check_commands = ["afni -help"] + +sanity_check_paths = { + 'files': ['bin/afni', 'lib/libgts.%s' % SHLIB_EXT, 'lib/libnifti2.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +modextrapaths = {'PATH': ['bin/scripts_for_r']} + +moduleclass = 'bio' From 6ab34120a223955f2cc551f0fb24d19fc2f8adec Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 26 Jan 2024 11:49:43 +0000 Subject: [PATCH 2/3] Updated to 24.0.2 which only got released a few days ago --- ...NI-24.0.01-foss-2023a.eb => AFNI-24.0.02-foss-2023a.eb} | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/a/AFNI/{AFNI-24.0.01-foss-2023a.eb => AFNI-24.0.02-foss-2023a.eb} (92%) diff --git a/easybuild/easyconfigs/a/AFNI/AFNI-24.0.01-foss-2023a.eb b/easybuild/easyconfigs/a/AFNI/AFNI-24.0.02-foss-2023a.eb similarity index 92% rename from easybuild/easyconfigs/a/AFNI/AFNI-24.0.01-foss-2023a.eb rename to easybuild/easyconfigs/a/AFNI/AFNI-24.0.02-foss-2023a.eb index 7926d97d997..265f24fc704 100644 --- a/easybuild/easyconfigs/a/AFNI/AFNI-24.0.01-foss-2023a.eb +++ b/easybuild/easyconfigs/a/AFNI/AFNI-24.0.02-foss-2023a.eb @@ -1,11 +1,10 @@ -# Updated to use CMake and better installation routines -# Updated to version 24.0.01 +# Updated to version 24.0.02 # Author: J. Sassmannshausen (Imperial College London/UK) easyblock = 'CMakeMake' name = 'AFNI' -version = '24.0.01' +version = '24.0.02' homepage = 'http://afni.nimh.nih.gov/' description = """AFNI is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - @@ -16,7 +15,7 @@ toolchainopts = {'openmp': True, 'pic': True} source_urls = ['https://github.com/afni/afni/archive/'] sources = ['AFNI_%(version)s.tar.gz'] -checksums = ['eb4135978bdf54be0ce1577b87c82ffe4ea4dfdeec21aa3a38e4a6929c9567b0'] +checksums = ['2915ed5bf98712abe3373bfc285f946fdee6cf1367e23ba80575dd6eedb3529a'] builddependencies = [ ('CMake', '3.26.3'), From 51292cb2610928a017683c5bc2a57f764d037fdc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 1 Apr 2024 23:41:10 +0200 Subject: [PATCH 3/3] Update easybuild/easyconfigs/a/AFNI/AFNI-24.0.02-foss-2023a.eb --- easybuild/easyconfigs/a/AFNI/AFNI-24.0.02-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AFNI/AFNI-24.0.02-foss-2023a.eb b/easybuild/easyconfigs/a/AFNI/AFNI-24.0.02-foss-2023a.eb index 265f24fc704..a1b2860e3fa 100644 --- a/easybuild/easyconfigs/a/AFNI/AFNI-24.0.02-foss-2023a.eb +++ b/easybuild/easyconfigs/a/AFNI/AFNI-24.0.02-foss-2023a.eb @@ -32,7 +32,7 @@ dependencies = [ ('libpng', '1.6.39'), ('libjpeg-turbo', '2.1.5.1'), ('GSL', '2.7'), - ('GLib', '2.77.1'), # must match version used in Qt5 (via PyQt5) + ('GLib', '2.77.1'), ('zlib', '1.2.13'), ('freeglut', '3.4.0'), ('Pillow', '10.0.0'),