Merge branch 'it4i-barbora'

l/libX11/libX11-1.6.3.eb

@@ -13,6 +13,7 @@ source_urls = [XORG_LIB_SOURCE]
 
 dependencies = [
     ('libxcb', '1.11.1'),
+    ('xtrans', '1.3.5'),
     ('fontconfig', '2.11.1'),
 ]
 

l/libxcb/libxcb-1.11.1.eb

@@ -23,31 +23,7 @@ dependencies = [
 ]
 
 sanity_check_paths = {
-    'files': [
+    'files': [],
-        'lib/libxcb%s.a' %
-        x for x in [
-            '',
-            '-local_composite',
-            '-damage',
-            '-dpms',
-            '-dri2',
-            '-glx',
-            '-randr',
-            '-record',
-            '-render',
-            '-res',
-            '-screensaver',
-            '-shape',
-            '-shm',
-            '-sync',
-            '-xevie',
-            '-xf86dri',
-            '-xfixes',
-            '-xinerama',
-            '-xprint',
-            '-xtest',
-            '-xv',
-            '-xvmc']],
     'dirs': [
         'include/xcb',
         'lib/pkgconfig'],

o/OpenFOAM/OpenFOAM-7-foss-2020a.eb

@@ -41,7 +41,7 @@ dependencies = [
 
 builddependencies = [
     ('Bison', '3.5.3'),
-    ('CMake', '3.9.0', '', True),
+    ('CMake', '3.16.4'),
     ('flex', '2.6.4'),
 ]
 

p/ParaView/ParaView-5.6.2-foss-2020a-Python-3.7.4-mpi.eb

@@ -0,0 +1,82 @@
+# JH 2020
+
+easyblock = 'CMakeMake'
+
+name = 'ParaView'
+version = '5.6.2'
+versionsuffix = '-Python-%(pyver)s-mpi'
+
+homepage = "https://www.paraview.org"
+description = "ParaView is a scientific parallel visualizer."
+
+toolchain = {'name': 'foss', 'version': '2020a'}
+toolchainopts = {'pic': True, 'usempi': True}
+
+local_download_suffix = 'download.php?submit=Download&version=v%(version_major_minor)s&type=source&os=all&downloadFile='
+source_urls = ['https://www.paraview.org/paraview-downloads/%s' % local_download_suffix]
+sources = ["ParaView-v%(version)s.tar.xz"]
+checksums = ['1f3710b77c58a46891808dbe23dc59a1259d9c6b7bb123aaaeaa6ddf2be882ea']
+
+dependencies = [
+    ('Python', '3.8.2'),
+    ('SciPy-bundle', '2020.03', '-Python-3.8.2'),
+    ('XZ', '5.2.5'),
+    ('HDF5', '1.10.6'),
+    ('netCDF', '4.7.4'),
+    ('libGLU', '9.0.1'),
+    ('X11', '20200222'),
+    ('Mesa', '20.0.2'),
+    ('Qt5', '5.14.1'),
+    ('zlib', '1.2.11'),
+    ('FFmpeg', '4.2.2'),
+    ('Szip', '2.1.1'),
+]
+
+builddependencies = [('CMake', '3.16.4')]
+
+separate_build_dir = True
+
+# Paraview
+configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DBUILD_SHARED_LIBS=ON '
+configopts += '-DPARAVIEW_QT_VERSION=5 -DQT_QMAKE_EXECUTABLE=$EBROOTQT5/bin/qmake '
+configopts += '-DPARAVIEW_USE_MPI=ON '
+configopts += '-DPARAVIEW_ENABLE_FFMPEG=ON '
+configopts += '-DPARAVIEW_ENABLE_PYTHON=ON '
+
+# Python
+configopts += "-DVTK_WRAP_PYTHON=ON "
+configopts += "-DVTK_PYTHON_VERSION=%(pyver)s "
+configopts += "-DPYTHON_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s "
+configopts += "-DPYTHON_LIBRARY=$EBROOTPYTHON/lib/libpython%%(pyshortver)s.%s " % SHLIB_EXT
+
+# Third party libs
+configopts += '-DVTK_USE_SYSTEM_MPI4PY=ON '
+configopts += "-DVTK_USE_SYSTEM_LZMA=ON "
+configopts += "-DVTK_USE_SYSTEM_HDF5=ON "
+configopts += "-DVTK_USE_SYSTEM_NETCDF=ON "
+
+# OpenGL & Mesa
+configopts += '-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s ' % SHLIB_EXT
+configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s ' % SHLIB_EXT
+configopts += '-DVTK_OPENGL_HAS_OSMESA=ON '
+configopts += '-DOSMESA_INCLUDE_DIR=$EBROOTMESA/include -DOSMESA_LIBRARY=$EBROOTMESA/lib/libOSMesa.%s ' % SHLIB_EXT
+
+
+# Without internet connection turn off testing (uncomment the following line)
+# configopts += '-DBUILD_TESTING=OFF '
+# Or consult https://gitlab.kitware.com/vtk/vtk/blob/master/Documentation/dev/git/data.md
+# and download ExternalData to $EASYBUILD_SOURCEPATH and adjust -DExternalData_OBJECT_STORES accordingly
+# Without internet connection, comment the following two lines (configopts and prebuildopts)
+configopts += '-DExternalData_OBJECT_STORES=%(builddir)s/ExternalData '
+
+# The ParaView server can be cranky, test downloads are quite often failing, especially in the case
+# of parallel downloads. Using ; insted of && gives a second chance to download the test files, if the
+# first serial attempt would fail.
+prebuildopts = 'make VTKData ;'
+
+sanity_check_paths = {
+    'files': ['bin/paraview'],
+    'dirs': ['include/paraview-%(version_major_minor)s', 'lib'],
+}
+
+moduleclass = 'vis'

r/RELION/RELION-3.1.0-gompi-2019b.eb

@@ -0,0 +1,33 @@
+# IT4Innovations 2020\
+# LK
+
+easyblock = 'CMakeMake'
+
+name = 'RELION'
+version = '3.1.0'
+
+homepage = 'http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page'
+description = """RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone local_computer
+ program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class
+ averages in electron cryo-microscopy (cryo-EM)."""
+
+toolchain = {'name': 'gompi', 'version': '2019b'}
+toolchainopts = {'opt': True}
+
+source_urls = ['https://github.com/3dem/relion/archive/']
+sources = ['%(version)s.tar.gz']
+
+builddependencies = [
+    ('CMake', '3.16.2', '', True),
+]
+
+dependencies = [
+    ('X11', '20190717', '', True),
+    ('libpng', '1.6.37', '', True),
+    ('FFTW', '3.3.8'),
+    ('FLTK', '1.3.5', '', True),
+]
+
+separate_build_dir = True
+
+moduleclass = 'bio'

r/RELION/RELION-3.1.0-intel-2020a.eb

@@ -0,0 +1,42 @@
+# IT4Innovations 2020
+# LK
+
+easyblock = 'CMakeMake'
+
+name = 'RELION'
+version = '3.1.0'
+
+homepage = 'http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page'
+description = """RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer
+ program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class
+ averages in electron cryo-microscopy (cryo-EM)."""
+
+toolchain = {'name': 'intel', 'version': '2020a'}
+
+source_urls = ['https://github.com/3dem/relion/archive/']
+sources = ['%(version)s.tar.gz']
+
+builddependencies = [('CMake', '3.16.2')]
+
+dependencies = [
+    ('X11', '20190717', '', ('GCCcore', '8.3.0')),
+    ('FLTK', '1.3.5', '', True),
+    ('LibTIFF', '4.1.0', '', ('GCCcore', '8.3.0')),
+#    ('tbb', '2019_U9', '', ('GCCcore', '8.3.0')),
+    ('FFTW', '3.3.8'),
+    ('GTK+', '3.24.13', '', ('GCCcore', '8.3.0')),
+    ('libXrender', '0.9.9', '', True),
+]
+
+#configopts = "-DCMAKE_SHARED_LINKER_FLAGS='-lpthread'  -DMPI_INCLUDE_PATH=$EBROOTIMPI/include64 "
+#configopts += "-DMPI_C_COMPILER=$EBROOTIMPI/bin64/mpiicc -DMPI_CXX_COMPILER=$EBROOTIMPI/bin64/mpiicpc "
+#configopts += "-DCUDA=OFF -DCudaTexture=OFF "
+#configopts += "-DALTCPU=ON -DMKLFFT=ON "
+#configopts += "-DALTCPU=ON -DMKLFFT=ON -DFORCE_OWN_TBB=OFF "
+
+sanity_check_paths = {
+    'files': ['bin/relion'],
+    'dirs': []
+}
+
+moduleclass = 'bio'