New foss2019b

foss-2019b/CDO-1.9.8-gompi-2019b.eb

@@ -0,0 +1,33 @@
+easyblock = 'ConfigureMake'
+
+name = 'CDO'
+version = '1.9.8'
+
+homepage = 'https://code.zmaw.de/projects/cdo'
+description = """CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data."""
+
+toolchain = {'name': 'gompi', 'version': '2019b'}
+toolchainopts = {'pic': True, 'usempi': True}
+
+source_urls = ['https://code.mpimet.mpg.de/attachments/download/20826/']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['f2660ac6f8bf3fa071cf2a3a196b3ec75ad007deb3a782455e80f28680c5252a']
+
+dependencies = [
+    ('HDF5', '1.10.5'),
+    ('netCDF', '4.7.1'),
+    ('YAXT', '0.6.2'),
+    ('ecCodes', '2.15.0'),
+]
+
+configopts = "--with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF --with-eccodes=$EBROOTECCODES"
+
+# fix for linking issues with HDF5 libraries for libcdi, should link with both -lnetcdf and -lhdf5_hl -lhdf5
+prebuildopts = "find libcdi -name Makefile | xargs sed -i 's/-lnetcdf -lnetcdf/-lnetcdf -lhdf5_hl -lhdf5/g' && "
+
+sanity_check_paths = {
+    'files': ['bin/cdo'],
+    'dirs': [],
+}
+
+moduleclass = 'data'

foss-2019b/ELIC_Python-1-foss-2019b-Python-3.7.4.eb

@@ -16,13 +16,12 @@ builddependencies = [
 dependencies = [
     ('Python', '3.7.4'),
     ('matplotlib', '3.1.1', versionsuffix),
-    #('GEOS', '3.8.0', versionsuffix),
     ('GDAL', '3.0.2', versionsuffix),
     #('NCL', '6.6.2'),
-    #('CDO', '1.9.7.1'),
-    #('NCO', '4.8.0'),
-    #('ncview', '2.1.7'),
-    #('libmo_unpack', '3.1.2'),
+    ('CDO', '1.9.7.1'),
+    ('NCO', '4.8.0'),
+    ('ncview', '2.1.7'),
+    ('libmo_unpack', '3.1.2'),
     ('orca', '1.3.0'),
 ]
 
@@ -44,9 +43,9 @@ exts_list = [
         'source_urls': ['https://sourceforge.net/projects/%(name)s/files/%(name)s/%(version)s'],
         'use_pip': True,
     }),
-    ('stratify', '0.2', {
+    ('stratify', '0.1.1', {
         'modulename': 'stratify',
-        'source_tmpl': 'master.zip',
+        'source_tmpl': 'v%(version)s.tar.gz',
         'source_urls': ['https://github.com/SciTools-incubator/python-stratify/archive/'],
     }),
     ('mo_pack', '0.2.0', {
@@ -54,9 +53,9 @@ exts_list = [
         'source_urls': ['https://github.com/SciTools/mo_pack/archive/'],
         'checksums': ['4aa70e1f846b666670843bc2514435dedf7393203e88abaf74d48f8f2717a726'],
     }),
-    ('basemap', '1.2.0', {
+    ('basemap', '1.2.1rel', {
         'modulename': 'mpl_toolkits',
-        'source_tmpl': 'basemap-master.zip',
+        'source_tmpl': 'v%(version)s.tar.gz',
         'source_urls': ['https://github.com/matplotlib/basemap/archive'],
         'use_pip': True,
     }),

foss-2019b/ELIC_R-1-foss-2019b-R-3.6.2.eb

@@ -123,9 +123,9 @@ modextrapaths = {'R_LIBS': ''}
 
 postinstallcmds = [
     "cd %(installdir)s && " +
-    'Rscript -e "install.packages(c(\'treemap\', \'ggmap\', \'hts\', \'thief\', \'forecastHybrid\', \'ggseas\', \'colourpicker\'), repos=\'https://www.freestatistics.org/cran/\', lib=\'%(installdir)s\')" && ' +
+    'Rscript -e "install.packages(c(\'treemap\', \'ggmap\', \'hts\', \'thief\', \'forecastHybrid\', \'ggseas\', \'colourpicker\', \'bsplus\', \'profvis\'), repos=\'https://www.freestatistics.org/cran/\', lib=\'%(installdir)s\')" && ' +
     'Rscript -e "library(remotes); install_github(\'myllym/GET\', lib=\'%(installdir)s\')" && ' +
-    'Rscript -e "install.packages(c(\'shinyFiles\', \'shinyjs\'), repos=\'http://cran.rstudio.com/\', lib=\'%(installdir)s\')"'
+    'Rscript -e "install.packages(c(\'shinyFiles\', \'shinyjs\', \'shinyhelper\', \'shinycssloaders\', \'shinyWidgets\', \'shinyBS\'), repos=\'http://cran.rstudio.com/\', lib=\'%(installdir)s\')"'
 ]
 
 sanity_check_paths = {

foss-2019b/ESMF-8.0.0-foss-2019b.eb

@@ -0,0 +1,31 @@
+name = 'ESMF'
+version = '8.0.0'
+
+homepage = 'https://sourceforge.net/projects/esmf'
+description = """The Earth System Modeling Framework (ESMF) is software for building and coupling weather,
+ climate, and related models."""
+
+toolchain = {'name': 'foss', 'version': '2019b'}
+toolchainopts = {'usempi': True}
+
+source_urls = [SOURCEFORGE_SOURCE]
+sources = ['%%(namelower)s_%s_src.tar.gz' % '_'.join(version.split('.'))]
+patches = ['ESMF-6.1.1_libopts.patch']
+checksums = [
+    '75c34c41806e703551b6b79566edf34c23f1eebcf821749e5320e860e565d94f',  # esmf_8_0_0_src.tar.gz
+    '3851627f07c32a7da55d99072d619942bd3a1d9dd002e1557716158e7aacdaf4',  # ESMF-6.1.1_libopts.patch
+]
+
+dependencies = [
+    ('netCDF', '4.7.1'),
+    ('netCDF-Fortran', '4.5.2'),
+    ('netCDF-C++4', '4.3.1'),
+]
+
+buildopts = 'ESMF_NETCDF_INCLUDE=$EBROOTNETCDFMINFORTRAN/include '
+buildopts += 'ESMF_NETCDF_LIBS="`nc-config --libs` `nf-config --flibs` `ncxx4-config --libs`"'
+
+# too parallel causes the build to become really slow
+maxparallel = 8
+
+moduleclass = 'geo'

foss-2019b/NCL-6.6.2-foss-2019b.eb

@@ -0,0 +1,49 @@
+name = 'NCL'
+version = '6.6.2'
+
+homepage = 'https://www.ncl.ucar.edu'
+description = "NCL is an interpreted language designed specifically for scientific data analysis and visualization."
+
+toolchain = {'name': 'foss', 'version': '2019b'}
+toolchainopts = {'cstd': 'c99', 'openmp': True, 'pic': True}
+
+source_urls = ['https://github.com/NCAR/ncl/archive/']
+sources = ['%(version)s.tar.gz']
+patches = ['NCL-6.4.0_fix-types.patch']
+checksums = [
+    'cad4ee47fbb744269146e64298f9efa206bc03e7b86671e9729d8986bb4bc30e',  # 6.6.2.tar.gz
+    'f6dfaf95e5de9045745e122cb44f9c035f81fab92f5892991ddfe93945891c8f',  # NCL-6.4.0_fix-types.patch
+]
+
+builddependencies = [
+    ('makedepend', '1.0.6'),
+    ('Bison', '3.3.2'),
+    ('flex', '2.6.4'),
+]
+osdependencies = [
+    ('csh')
+]
+dependencies = [
+    ('cURL', '7.66.0'),
+    ('JasPer', '2.0.14'),
+    ('g2lib', '3.1.0'),
+    ('g2clib', '1.6.0'),
+    ('HDF', '4.2.14'),
+    ('HDF5', '1.10.5'),
+    ('netCDF', '4.7.1'),
+    ('netCDF-Fortran', '4.5.2'),
+    ('Szip', '2.1.1'),
+    ('freetype', '2.10.1'),
+    ('zlib', '1.2.11'),
+    ('GDAL', '3.0.2', '-Python-3.7.4'),
+    ('UDUNITS', '2.2.26'),
+    ('ESMF', '8.0.0'),
+    ('bzip2', '1.0.8'),
+    ('cairo', '1.16.0'),
+    ('libiconv', '1.16'),
+    ('GSL', '2.6'),
+    ('libpng', '1.6.37'),
+    ('libjpeg-turbo', '2.0.3'),
+]
+
+moduleclass = 'data'

foss-2019b/NCO-4.9.1-foss-2019b.eb

@@ -0,0 +1,35 @@
+easyblock = 'ConfigureMake'
+
+name = 'NCO'
+version = '4.9.1'
+
+homepage = "http://nco.sourceforge.net"
+description = """manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5"""
+
+toolchain = {'name': 'foss', 'version': '2019b'}
+
+source_urls = ['https://github.com/nco/nco/archive/']
+sources = ['%(version)s.tar.gz']
+
+builddependencies = [
+    ('Bison', '3.3.2'),
+    ('flex', '2.6.4'),
+]
+
+dependencies = [
+    ('UDUNITS', '2.2.26'),
+    ('expat', '2.2.7'),
+    ('ANTLR', '2.7.7'),
+    ('libdap', '3.20.6'),
+    ('GSL', '2.6'),
+    ('netCDF', '4.7.1'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/nc%s' % x for x in ('ap2', 'atted', 'bo', 'diff', 'ea', 'ecat', 'es',
+                                       'flint', 'ks', 'pdq', 'ra', 'rcat', 'rename', 'wa')] +
+             ['lib/libnco.a', 'lib/libnco.%s' % SHLIB_EXT, 'lib/libnco_c++.a', 'lib/libnco_c++.%s' % SHLIB_EXT],
+    'dirs': ['include'],
+}
+
+moduleclass = 'tools'

foss-2019b/YAXT-0.6.2-gompi-2019b.eb

@@ -0,0 +1,23 @@
+easyblock = 'ConfigureMake'
+
+name = 'YAXT'
+version = '0.6.2'
+
+homepage = 'https://www.dkrz.de/redmine/projects/yaxt'
+description = "Yet Another eXchange Tool"
+
+toolchain = {'name': 'gompi', 'version': '2019b'}
+toolchainopts = {'usempi': True}
+
+source_urls = ['https://www.dkrz.de/redmine/attachments/download/492/']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['7fc9b3e5dd2e0d3d5846f389a01c935aa40528eb09d82162b76c061b496a3c5b']
+
+configopts = 'FC="$F90" FCFLAGS="$F90FLAGS -cpp"'
+
+sanity_check_paths = {
+    'files': ['include/yaxt.h', 'include/yaxt.mod', 'lib/libyaxt.a', 'lib/libyaxt.%s' % SHLIB_EXT],
+    'dirs': ['include/xt'],
+}
+
+moduleclass = 'tools'

foss-2019b/ecCodes-2.15.0-gompi-2019b.eb

@@ -0,0 +1,34 @@
+easyblock = 'CMakeMake'
+
+name = 'ecCodes'
+version = '2.15.0'
+
+homepage = 'https://software.ecmwf.int/wiki/display/ECC/ecCodes+Home'
+description = """ecCodes is a package developed by ECMWF which provides an application programming interface and
+ a set of tools for decoding and encoding messages in the following formats: WMO FM-92 GRIB edition 1 and edition 2,
+ WMO FM-94 BUFR edition 3 and edition 4, WMO GTS abbreviated header (only decoding)."""
+
+toolchain = {'name': 'gompi', 'version': '2019b'}
+
+source_urls = ['https://confluence.ecmwf.int/download/attachments/45757960/']
+sources = ['eccodes-%(version)s-Source.tar.gz']
+checksums = ['9fec8ad11f380795af632fb3105c4aa37d30f22fa70dba48fd93324cf6388d59']
+
+builddependencies = [('CMake', '3.15.3')]
+dependencies = [
+    ('netCDF', '4.7.1'),
+    ('JasPer', '2.0.14'),
+]
+
+separate_build_dir = True
+
+configopts = "-DENABLE_NETCDF=ON -DENABLE_JPG=ON -DENABLE_PYTHON=OFF"
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in ['bufr_copy', 'bufr_dump', 'bufr_filter', 'bufr_ls',
+                                     'codes_count', 'codes_info', 'codes_split_file',
+                                     'grib_copy', 'grib_dump', 'grib_filter', 'grib_ls']],
+    'dirs': [],
+}
+
+moduleclass = 'tools'

foss-2019b/libmo_unpack-3.1.2-foss-2019b.eb

@@ -0,0 +1,25 @@
+easyblock = 'CMakeMake'
+
+name = 'libmo_unpack'
+version = '3.1.2'
+
+homepage = 'https://github.com/SciTools/libmo_unpack'
+description = """A library for handling the WGDOS and RLE compression schemes used in UM files."""
+
+toolchain = {'name': 'foss', 'version': '2019b'}
+
+source_urls = ['https://github.com/SciTools/libmo_unpack/archive']
+sources = ['v%(version)s.tar.gz']
+
+builddependencies = [('CMake', '3.15.3')]
+
+separate_build_dir = True
+
+configopts = '-DCMAKE_EXE_LINKER_FLAGS="$LDFLAGS -lsubunit"'
+
+sanity_check_paths = {
+    'files': ['lib/libmo_unpack.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'tools'

foss-2019b/ncview-2.1.7-gompi-2019b.eb

@@ -12,14 +12,14 @@ name = 'ncview'
 version = '2.1.7'
 
 homepage = 'http://meteora.ucsd.edu/~pierce/ncview_home_page.html'
-description = """Ncview is a visual browser for netCDF format files. 
-Typically you would use ncview to get a quick and easy, push-button 
-look at your netCDF files. You can view simple movies of the data, 
-view along various dimensions, take a look at the actual data values, 
+description = """Ncview is a visual browser for netCDF format files.
+Typically you would use ncview to get a quick and easy, push-button
+look at your netCDF files. You can view simple movies of the data,
+view along various dimensions, take a look at the actual data values,
 change color maps, invert the data, etc."""
 
-toolchain = {'name': 'gompi', 'version': '2019a'}
-toolchainopts = {'opt': True, 'pic': True, 'usempi': True}
+toolchain = {'name': 'gompi', 'version': '2019b'}
+toolchainopts = {'usempi': True, 'pic': True}
 
 source_urls = ['ftp://cirrus.ucsd.edu/pub/ncview/']
 sources = [SOURCE_TAR_GZ]
@@ -31,10 +31,10 @@ configopts = "--with-udunits2_incdir=$EBROOTUDUNITS/include --with-udunits2_libd
 configopts += "--with-nc-config=$EBROOTNETCDF/bin/nc-config"
 
 dependencies = [
-    ('netCDF', '4.6.2'),
-    ('netCDF-Fortran', '4.4.5'),
+    ('netCDF', '4.7.1'),
+    ('netCDF-Fortran', '4.5.2'),
     ('UDUNITS', '2.2.26'),
-    ('X11', '20190311'),
+    ('X11', '20190717'),
     ('zlib', '1.2.11'),
 ]
 

foss-2019b/netCDF-C++4-4.3.1-gompi-2019b.eb

@@ -0,0 +1,25 @@
+easyblock = 'ConfigureMake'
+
+name = 'netCDF-C++4'
+version = '4.3.1'
+
+homepage = 'https://www.unidata.ucar.edu/software/netcdf/'
+description = """NetCDF (network Common Data Form) is a set of software libraries
+ and machine-independent data formats that support the creation, access, and sharing of array-oriented
+ scientific data."""
+
+toolchain = {'name': 'gompi', 'version': '2019b'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/Unidata/netcdf-cxx4/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['e3fe3d2ec06c1c2772555bf1208d220aab5fee186d04bd265219b0bc7a978edc']
+
+dependencies = [('netCDF', '4.7.1')]
+
+sanity_check_paths = {
+    'files': ['include/netcdf', 'lib/libnetcdf_c++4.a', 'lib/libnetcdf_c++4.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'data'