Upgrade foss-2017b

foss-2017b/exactextract-0.1-foss-2017b.eb

@@ -0,0 +1,31 @@
+easyblock = 'CMakeMake'
+
+name = 'exactextract'
+version = '0.1'
+
+homepage = 'https://github.com/isciences/exactextract'
+description = """exactextract provides a fast and accurate algorithm for summarizing values in the portion of a raster dataset that is covered by a polygon, often referred to as zonal statistics. Unlike other zonal statistics implementations, it takes into account raster cells that are partially covered by the polygon."""
+
+toolchain = {'name': 'foss', 'version': '2017b'}
+
+source_urls = ['https://github.com/isciences/exactextract/archive/']
+sources = ['master.zip']
+
+builddependencies = [('CMake', '3.11.4')]
+dependencies = [
+    ('GEOS', '3.6.2', '-Python-2.7.14'),
+    ('GDAL', '2.2.3', '-Python-2.7.14'),
+]
+
+separate_build_dir = True
+
+configopts = '-DCMAKE_BUILD_TYPE=Release'
+
+#CMAKE_INSTALL_PREFIX
+
+sanity_check_paths = {
+    'files': ['bin/exactextract'],
+    'dirs': [],
+}
+
+moduleclass = 'tools'

foss-2017b/nodejs-8.9.4-foss-2017b.eb

@@ -0,0 +1,28 @@
+easyblock = 'ConfigureMake'
+
+name = 'nodejs'
+version = '8.9.4'
+
+homepage = 'http://nodejs.org'
+
+description = """Node.js is a platform built on Chrome's JavaScript runtime 
+ for easily building fast, scalable network applications. Node.js uses an 
+ event-driven, non-blocking I/O model that makes it lightweight and efficient, 
+ perfect for data-intensive real-time applications that run across distributed devices."""
+
+toolchain = {'name': 'foss', 'version': '2017b'}
+toolchainopts = {'lowopt': True}
+
+sources = ['node-v%(version)s.tar.gz']
+source_urls = ['http://nodejs.org/dist/v%(version)s/']
+checksums = ['729b44b32b2f82ecd5befac4f7518de0c4e3add34e8fe878f745740a66cbbc01']
+
+# Python is required (only) as build dependency
+allow_system_deps = [('Python', SYS_PYTHON_VERSION)]
+
+sanity_check_paths = {
+    'files': ["bin/node", "bin/npm"],
+    'dirs': ["lib/node_modules", "include/node"]
+}
+
+moduleclass = 'lang'

foss-2017b/pktools-2.6.7-foss-2017b.eb

@@ -0,0 +1,34 @@
+easyblock = 'CMakeMake'
+
+name = 'pktools'
+version = '2.6.7'
+
+homepage = 'http://pktools.nongnu.org/html/index.html'
+description = """pktools is a suite of utilities written in C++ for image processing with a focus on remote sensing applications. 
+ It relies on the Geospatial Data Abstraction Library (GDAL, http://www.gdal.org) and OGR."""
+
+toolchain = {'name': 'foss', 'version': '2017b'}
+
+source_urls = ['http://download.savannah.gnu.org/releases/pktools/']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['15c3e8fb5bc92b1205e99a958daf5eec']
+
+builddependencies = [('CMake', '3.11.4')]
+dependencies = [
+    ('GDAL', '2.2.3', '-Python-2.7.14'),
+    ('GSL','2.4'),
+    ('Armadillo', '8.300.1'),
+    #('OpenBLAS','0.3.1'),
+]
+
+separate_build_dir = True
+
+#configopts = '-DBUILD_WITH_LIBLAS=ON'
+#configopts += 'LIBLAS_LIBRARY="$EBROOTOPENBLAS" LIBLAS_INCLUDE_DIR="$EBROOTOPENBLAS/include" LIBLAS_C_LIBRARY="$EBROOTOPENBLAS/lib"'
+
+sanity_check_paths = {
+    'files': ['bin/pktools-config', 'lib/libalgorithms.a', 'lib/libbase.a', 'lib/libfileClasses.a', 'lib/libimageClasses.a'],
+    'dirs': [],
+}
+
+moduleclass = 'tools'

intel-2018/PyQt5-5.8.2-intel-2018-Python-2.7.13.eb

@@ -0,0 +1,34 @@
+easyblock = 'ConfigureMakePythonPackage'
+
+name = 'PyQt5'
+version = '5.8.2'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'http://www.riverbankcomputing.co.uk/software/pyqt'
+description = """PyQt5 is a set of Python bindings for v5 of the Qt application framework from The Qt Company."""
+
+toolchain = {'name': 'intel', 'version': '2018'}
+
+source_urls = ['http://sourceforge.net/projects/pyqt/files/PyQt5/PyQt-%(version)s']
+sources = ['%(name)s_gpl-%(version)s.tar.gz']
+
+dependencies = [
+    ('Python', '2.7.13'),
+    ('SIP', '4.19.2', versionsuffix),
+    ('Qt5', '5.8.0'),
+]
+
+configopts = "configure.py --confirm-license"
+configopts += " --destdir=%(installdir)s/lib/python%(pyshortver)s/site-packages "
+configopts += " --no-sip-files"
+
+options = {'modulename': '%(name)s'}
+
+modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'],
+}
+
+moduleclass = 'vis'

intel-2018/SIP-4.19.2-intel-2018-Python-2.7.13.eb

@@ -0,0 +1,30 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Author: Bart Verleye
+# Center for eResearch, Auckland
+easyblock = 'ConfigureMakePythonPackage'
+
+name = 'SIP'
+version = '4.19.2'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'http://www.riverbankcomputing.com/software/sip/'
+description = """SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries."""
+
+toolchain = {'name': 'intel', 'version': '2018'}
+
+sources = [SOURCELOWER_TAR_GZ]
+source_urls = ['http://sourceforge.net/projects/pyqt/files/sip/sip-%(version)s']
+
+dependencies = [('Python', '2.7.13')]
+
+configopts = "configure.py --bindir %(installdir)s/bin --incdir %(installdir)s/include "
+configopts += "--destdir %(installdir)s/lib/python%(pyshortver)s/site-packages"
+
+sanity_check_paths = {
+    'files': ['bin/sip', 'include/sip.h'] +
+             ['lib/python%%(pyshortver)s/site-packages/%s' % x
+              for x in ['sip.%s' % SHLIB_EXT, 'sipconfig.py', 'sipdistutils.py']],
+    'dirs': [],
+}
+
+moduleclass = 'lang'

intel-2018/nodejs-8.9.4-intel-2018-Python-2.7.13.eb

@@ -0,0 +1,41 @@
+easyblock = 'ConfigureMake'
+
+name = 'nodejs'
+version = '8.9.4'
+versionsuffix = '-Python-2.7.13'
+
+homepage = 'http://nodejs.org'
+
+description = """Node.js is a platform built on Chrome's JavaScript runtime 
+ for easily building fast, scalable network applications. Node.js uses an 
+ event-driven, non-blocking I/O model that makes it lightweight and efficient, 
+ perfect for data-intensive real-time applications that run across distributed devices."""
+
+toolchain = {'name': 'intel', 'version': '2018'}
+toolchainopts = {'lowopt': True}
+
+sources = ['node-v%(version)s.tar.gz']
+source_urls = ['http://nodejs.org/dist/v%(version)s/']
+checksums = ['729b44b32b2f82ecd5befac4f7518de0c4e3add34e8fe878f745740a66cbbc01']
+
+pyver = '2.7.13'
+pyshortver = '.'.join(pyver.split('.')[0:2])
+
+# Python is required (only) as build dependency
+builddependencies = [
+    ('Python', pyver),
+]
+
+modextrapaths = {
+    'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages', 'lib64/python%(pyshortver)s/site-packages'],
+}
+
+# Python is required (only) as build dependency
+#allow_system_deps = [('Python', SYS_PYTHON_VERSION)]
+
+sanity_check_paths = {
+    'files': ["bin/node", "bin/npm"],
+    'dirs': ["lib/node_modules", "include/node"]
+}
+
+moduleclass = 'lang'

intel-2018/poppler-0.70.1-intel-2018.eb

@@ -0,0 +1,53 @@
+# easybuild easyconfig
+#
+# John Dey jfdey@fredhutch.org
+# Fred Hutchinson Cancer Research Center Seattle WA USA
+
+easyblock = 'CMakeMake'
+
+name = 'poppler'
+version = '0.70.1'
+
+homepage = 'https://poppler.freedesktop.org/'
+description = """Poppler is a PDF rendering library based on the xpdf-3.0 code
+ base."""
+
+toolchain = {'name': 'foss', 'version': '2018b'}
+
+source_urls = ['https://poppler.freedesktop.org/']
+sources = [SOURCELOWER_TAR_XZ]
+checksums = ['66972047d9ef8162cc8c389d7e7698291dfc9f2b3e4ea9a9f08ae604107451bd']
+
+separate_build_dir = True
+
+builddependencies = [
+    ('pkgconfig', '1.3.1', '-Python-2.7.15'),
+    ('binutils', '2.30'),
+    ('CMake', '3.11.4'),
+    ('Qt5', '5.10.1'),
+    ('cairo', '1.14.12'),
+    ('GObject-Introspection', '1.54.1', '-Python-2.7.15'),
+    ('libjpeg-turbo', '2.0.0'),
+    ('libpng', '1.6.34'),
+    ('LibTIFF', '4.0.9'),
+    ('NSS', '3.39'),
+    ('OpenJPEG', '2.3.0'),
+]
+
+bin_files = ['pdfdetach', 'pdffonts', 'pdfimages', 'pdfinfo', 'pdfseparate',
+             'pdftocairo', 'pdftohtml', 'pdftoppm', 'pdftops', 'pdftotext',
+             'pdfunite']
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in bin_files] +
+             ['lib/libpoppler.%s' % SHLIB_EXT,
+              'lib/libpoppler-cpp.%s' % SHLIB_EXT,
+              'lib/libpoppler-glib.%s' % SHLIB_EXT,
+              'include/poppler/glib/poppler.h'],
+    'dirs': ['bin',
+             'include',
+             'include/poppler/glib',
+             ]
+}
+
+moduleclass = 'vis'