From d3cb8adf17eb80b6bdf66eee369b4a946df1e743 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Thu, 9 Jan 2020 11:14:33 +0100 Subject: [PATCH] new file: b/Biopython/Biopython-1.76-Py-3.7.eb new file: b/bzip2/bzip2-1.0.8.eb new file: c/Cython/Cython-0.29.14-Py-3.7.eb new file: c/cairo/cairo-1.17.2.eb modified: e/Eigen/Eigen-3.3.7.eb new file: g/GLib/GLib-2.62.4.eb new file: l/libffi/libffi-3.3.eb new file: "l/libpng/\\" new file: l/libpng/libpng-1.6.37.eb new file: m/Meson/Meson-0.51.2-Py-3.7.eb new file: m/Meson/Meson-0.53.0-Py-3.7.eb new file: n/Ninja/Ninja-1.9.0-Py-3.7.eb modified: n/numpy/numpy-1.18.1-Py-3.6.eb new file: n/numpy/numpy-1.18.1-Py-3.7.eb modified: o/OpenBabel/OpenBabel-2.4.9-GCCcore-6.3.0-Python-3.7.3.eb new file: o/OpenBabel/OpenBabel-3.0.0-Py-3.7.eb new file: p/PCRE/PCRE-8.43.eb modified: p/Py/Py-3.7.eb new file: p/Python/Python-3.7.5-GCC-8.3.0-2.32-base.eb new file: p/phono3py/phono3py-1.18.2-conda.eb new file: p/phonopy/phono3py-1.18.2-conda.eb new file: p/phonopy/phonopy-2.4.2-conda.eb new file: p/pixman/pixman-0.38.4.eb new file: s/SQLite/SQLite-3.30.1.eb new file: s/SWIG/SWIG-3.0.12-Py-3.7.eb new file: s/SWIG/SWIG-4.0.1-Py-3.7.eb new file: t/Tcl/Tcl-8.6.10.eb new file: u/util-linux/util-linux-2.34.eb deleted: p/phono3py/phono3py-1.18.2-Py-3.6.eb --- b/Biopython/Biopython-1.76-Py-3.7.eb | 32 +++++++++ b/bzip2/bzip2-1.0.8.eb | 33 +++++++++ c/Cython/Cython-0.29.14-Py-3.7.eb | 22 ++++++ c/cairo/cairo-1.17.2.eb | 68 +++++++++++++++++++ e/Eigen/Eigen-3.3.7.eb | 2 +- g/GLib/GLib-2.62.4.eb | 44 ++++++++++++ l/libffi/libffi-3.3.eb | 31 +++++++++ "l/libpng/\\" | 23 +++++++ l/libpng/libpng-1.6.37.eb | 23 +++++++ m/Meson/Meson-0.51.2-Py-3.7.eb | 30 ++++++++ m/Meson/Meson-0.53.0-Py-3.7.eb | 30 ++++++++ n/Ninja/Ninja-1.9.0-Py-3.7.eb | 26 +++++++ n/numpy/numpy-1.18.1-Py-3.6.eb | 4 +- n/numpy/numpy-1.18.1-Py-3.7.eb | 32 +++++++++ ...nBabel-2.4.9-GCCcore-6.3.0-Python-3.7.3.eb | 2 +- o/OpenBabel/OpenBabel-3.0.0-Py-3.7.eb | 39 +++++++++++ p/PCRE/PCRE-8.43.eb | 20 ++++++ p/Py/Py-3.7.eb | 8 +-- p/Python/Python-3.7.5-GCC-8.3.0-2.32-base.eb | 62 +++++++++++++++++ p/phono3py/phono3py-1.18.2-Py-3.6.eb | 25 ------- p/phono3py/phono3py-1.18.2-conda.eb | 26 +++++++ p/phonopy/phono3py-1.18.2-conda.eb | 26 +++++++ p/phonopy/phonopy-2.4.2-conda.eb | 26 +++++++ p/pixman/pixman-0.38.4.eb | 22 ++++++ s/SQLite/SQLite-3.30.1.eb | 39 +++++++++++ s/SWIG/SWIG-3.0.12-Py-3.7.eb | 20 ++++++ s/SWIG/SWIG-4.0.1-Py-3.7.eb | 20 ++++++ t/Tcl/Tcl-8.6.10.eb | 27 ++++++++ u/util-linux/util-linux-2.34.eb | 45 ++++++++++++ 29 files changed, 774 insertions(+), 33 deletions(-) create mode 100644 b/Biopython/Biopython-1.76-Py-3.7.eb create mode 100644 b/bzip2/bzip2-1.0.8.eb create mode 100644 c/Cython/Cython-0.29.14-Py-3.7.eb create mode 100644 c/cairo/cairo-1.17.2.eb create mode 100644 g/GLib/GLib-2.62.4.eb create mode 100644 l/libffi/libffi-3.3.eb create mode 100644 "l/libpng/\\" create mode 100644 l/libpng/libpng-1.6.37.eb create mode 100644 m/Meson/Meson-0.51.2-Py-3.7.eb create mode 100644 m/Meson/Meson-0.53.0-Py-3.7.eb create mode 100644 n/Ninja/Ninja-1.9.0-Py-3.7.eb create mode 100644 n/numpy/numpy-1.18.1-Py-3.7.eb create mode 100644 o/OpenBabel/OpenBabel-3.0.0-Py-3.7.eb create mode 100644 p/PCRE/PCRE-8.43.eb create mode 100644 p/Python/Python-3.7.5-GCC-8.3.0-2.32-base.eb delete mode 100644 p/phono3py/phono3py-1.18.2-Py-3.6.eb create mode 100644 p/phono3py/phono3py-1.18.2-conda.eb create mode 100644 p/phonopy/phono3py-1.18.2-conda.eb create mode 100644 p/phonopy/phonopy-2.4.2-conda.eb create mode 100644 p/pixman/pixman-0.38.4.eb create mode 100644 s/SQLite/SQLite-3.30.1.eb create mode 100644 s/SWIG/SWIG-3.0.12-Py-3.7.eb create mode 100644 s/SWIG/SWIG-4.0.1-Py-3.7.eb create mode 100644 t/Tcl/Tcl-8.6.10.eb create mode 100644 u/util-linux/util-linux-2.34.eb diff --git a/b/Biopython/Biopython-1.76-Py-3.7.eb b/b/Biopython/Biopython-1.76-Py-3.7.eb new file mode 100644 index 00000000..a9fa574b --- /dev/null +++ b/b/Biopython/Biopython-1.76-Py-3.7.eb @@ -0,0 +1,32 @@ +# IT4Innovations 2019 + +easyblock = "PythonPackage" +name = 'Biopython' +version = '1.76' + +homepage = 'http://www.biopython.org' +description = """Biopython is a set of freely available tools for biological + local_computation written in Python by an international team of developers. It is + a distributed collaborative effort to develop Python libraries and + applications which address the needs of current and future work in + bioinformatics. """ + +toolchain = {'name': 'Py', 'version': '3.7'} + +source_urls = ['http://biopython.org/DIST'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('numpy', '1.18.1'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python3.7/site-packages/%(namelower)s-%(version)s-py3.7.egg-info'], +} + +sanity_check_commands = ["python -c 'import Bio.MarkovModel'"] + +options = {'modulename': 'Bio'} + +moduleclass = 'python' diff --git a/b/bzip2/bzip2-1.0.8.eb b/b/bzip2/bzip2-1.0.8.eb new file mode 100644 index 00000000..bc1710a1 --- /dev/null +++ b/b/bzip2/bzip2-1.0.8.eb @@ -0,0 +1,33 @@ +# IT4Innovations 2019 +name = 'bzip2' +version = '1.0.8' + +homepage = 'https://sourceware.org/bzip2' + +description = """ + bzip2 is a freely available, patent free, high-quality data compressor. It + typically compresses files to within 10% to 15% of the best available + techniques (the PPM family of statistical compressors), whilst being around + twice as fast at compression and six times faster at decompression. +""" + +toolchain = SYSTEM +toolchainopts = {'pic': True} + +source_urls = ['https://sourceware.org/pub/bzip2/'] +sources = [SOURCE_TAR_GZ] +patches = ['bzip2-1.0.6-pkgconfig.patch'] +checksums = [ + 'ab5a03176ee106d3f0fa90e381da478ddae405918153cca248e682cd0c4a2269', # bzip2-1.0.8.tar.gz + '5a823e820b332eca3684416894f58edc125ac3dace9f46e62f98e45362aa8a6d', # bzip2-1.0.6-pkgconfig.patch +] + +builddependencies = [ + ('CMake', '3.16.2'), +] + +buildopts = 'CC="gcc" CFLAGS="-fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64"' + +parallel = 1 + +moduleclass = 'tools' diff --git a/c/Cython/Cython-0.29.14-Py-3.7.eb b/c/Cython/Cython-0.29.14-Py-3.7.eb new file mode 100644 index 00000000..f0659235 --- /dev/null +++ b/c/Cython/Cython-0.29.14-Py-3.7.eb @@ -0,0 +1,22 @@ +# IT4Innovations 2020 + +easyblock = 'PythonPackage' + +name = 'Cython' +version = '0.29.14' + +homepage = 'https://pypi.python.org/pypi/Cython/' +description = """The Cython language makes writing C extensions for the Python language as easy as Python itself. +Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and optimizations.""" + +toolchain = {'name': 'Py', 'version': '3.7'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/cygdb', 'bin/cython', 'bin/cythonize'], + 'dirs': ['bin', 'lib'] +} + +moduleclass = 'lang' diff --git a/c/cairo/cairo-1.17.2.eb b/c/cairo/cairo-1.17.2.eb new file mode 100644 index 00000000..cc66ecc2 --- /dev/null +++ b/c/cairo/cairo-1.17.2.eb @@ -0,0 +1,68 @@ +# IT4Innovations 2020 + +easyblock = 'ConfigureMake' + +name = 'cairo' +version = '1.17.2' + +homepage = 'http://cairographics.org' +description = """Cairo is a 2D graphics library with support for multiple output devices. + Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, + PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB""" + +toolchain = SYSTEM + +source_urls = ['https://cairographics.org/snapshots/'] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), + ('libpng', '1.6.37'), +# ('freetype', '2.7.1', '-libpng-1.6.29'), + ('pixman', '0.38.4'), +# ('expat', '2.2.0'), + ('GLib', '2.62.4'), + ('X11', '20190717'), +] + +# disable symbol lookup, which requires -lbfd, to avoid link issues with +# (non-PIC) libiberty.a provided by GCC +configopts = "--enable-symbol-lookup=no --enable-gobject=yes --enable-svg=yes --enable-tee=yes --enable-xlib-xcb " + +# workaround for "hidden symbol .* in .* is referenced by DSO" and "ld: +# final link failed: Bad value" +buildopts = 'LD="$CC" LDFLAGS="$LDFLAGS"' + +sanity_check_paths = { + 'files': [ + 'bin/cairo-trace', + 'lib/cairo/libcairo-trace.so', + 'lib/cairo/libcairo-trace.a', + 'lib/libcairo.a', + 'lib/libcairo-gobject.a', + 'lib/libcairo-script-interpreter.a', + 'lib/libcairo-gobject.so', + 'lib/libcairo-script-interpreter.so', + 'lib/libcairo.so'] + + [ + 'include/cairo/cairo%s.h' % + x for x in [ + '', + '-deprecated', + '-features', + '-ft', + '-gobject', + '-pdf', + '-ps', + '-script', + '-script-interpreter', + '-svg', + '-version', + '-xcb', + '-xlib', + '-xlib-xrender']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'vis' diff --git a/e/Eigen/Eigen-3.3.7.eb b/e/Eigen/Eigen-3.3.7.eb index 46e89bfa..390759b6 100644 --- a/e/Eigen/Eigen-3.3.7.eb +++ b/e/Eigen/Eigen-3.3.7.eb @@ -13,7 +13,7 @@ source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] dependencies = [ - ('CMake', '3.13.1'), + ('CMake', '3.16.2'), ] moduleclass = 'math' diff --git a/g/GLib/GLib-2.62.4.eb b/g/GLib/GLib-2.62.4.eb new file mode 100644 index 00000000..620266b6 --- /dev/null +++ b/g/GLib/GLib-2.62.4.eb @@ -0,0 +1,44 @@ +# IT4Innovations 2020 + +easyblock = 'MesonNinja' + +name = 'GLib' +version = '2.62.4' + +homepage = 'http://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = SYSTEM +toolchainopts = {'pic': True} + +source_urls = ['http://ftp.gnome.org/pub/gnome/sources/glib/%(version_major_minor)s/'] +sources = ['glib-%(version)s.tar.xz'] + +builddependencies = [ + ('Meson', '0.53.0', '', ('Py', '3.7')), + ('Ninja', '1.9.0', '', ('Py', '3.7')), + ('binutils', '2.32'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('libffi', '3.2.1'), + ('gettext', '0.20.1'), + ('libxml2', '2.9.9'), + ('PCRE', '8.43'), + ('util-linux', '2.34'), +] + +# avoid using hardcoded path to Python binary in build step +preconfigopts = "export PYTHON=python && " + +configopts = "--buildtype=release --default-library=both " + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['lib/libglib-%(version_major)s.0.a', 'lib/libglib-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include'], +} + +moduleclass = 'vis' diff --git a/l/libffi/libffi-3.3.eb b/l/libffi/libffi-3.3.eb new file mode 100644 index 00000000..0dc5e067 --- /dev/null +++ b/l/libffi/libffi-3.3.eb @@ -0,0 +1,31 @@ +# IT4Innovations 2020 + +easyblock = 'ConfigureMake' + +name = 'libffi' +version = '3.3' + +homepage = 'http://sourceware.org/libffi/' +description = """The libffi library provides a portable, high level programming interface to various calling +conventions. This allows a programmer to call any function specified by a call interface description at run-time.""" + +toolchain = SYSTEM + +source_urls = [ + 'ftp://sourceware.org/pub/libffi/', + 'http://www.mirrorservice.org/sites/sourceware.org/pub/libffi/', +] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': [ + ('lib/libffi.%s' % + SHLIB_EXT, + 'lib64/libffi.%s' % + SHLIB_EXT), + ('lib/libffi.a', + 'lib64/libffi.a')], + 'dirs': [], +} + +moduleclass = 'lib' diff --git "a/l/libpng/\\" "b/l/libpng/\\" new file mode 100644 index 00000000..ad3dc441 --- /dev/null +++ "b/l/libpng/\\" @@ -0,0 +1,23 @@ +# IT4Innovations 2020 + +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.37' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = SYSTEM +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.11')] + +preconfigopts = 'export LDFLAGS="-L/apps/all/zlib/1.2.11/lib" CPPFLAGS="-I/apps/all/zlib/1.2.11/include" &&' + +configopts = "--with-pic" + +moduleclass = 'lib' diff --git a/l/libpng/libpng-1.6.37.eb b/l/libpng/libpng-1.6.37.eb new file mode 100644 index 00000000..ad3dc441 --- /dev/null +++ b/l/libpng/libpng-1.6.37.eb @@ -0,0 +1,23 @@ +# IT4Innovations 2020 + +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.37' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = SYSTEM +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.11')] + +preconfigopts = 'export LDFLAGS="-L/apps/all/zlib/1.2.11/lib" CPPFLAGS="-I/apps/all/zlib/1.2.11/include" &&' + +configopts = "--with-pic" + +moduleclass = 'lib' diff --git a/m/Meson/Meson-0.51.2-Py-3.7.eb b/m/Meson/Meson-0.51.2-Py-3.7.eb new file mode 100644 index 00000000..cae93f8c --- /dev/null +++ b/m/Meson/Meson-0.51.2-Py-3.7.eb @@ -0,0 +1,30 @@ +# IT4Innovations 2019 + +easyblock = 'PythonPackage' + +name = 'Meson' +version = '0.51.2' + +homepage = 'https://mesonbuild.com' +description = "Meson is a cross-platform build system designed to be both as fast and as user friendly as possible." + +toolchain = {'name': 'Py', 'version': '3.7'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Ninja', '1.9.0'), +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': 'mesonbuild'} + +sanity_check_paths = { + 'files': ['bin/meson'], + 'dirs': ['lib/python3.7/site-packages'], +} + +moduleclass = 'tools' diff --git a/m/Meson/Meson-0.53.0-Py-3.7.eb b/m/Meson/Meson-0.53.0-Py-3.7.eb new file mode 100644 index 00000000..8d5cc8d0 --- /dev/null +++ b/m/Meson/Meson-0.53.0-Py-3.7.eb @@ -0,0 +1,30 @@ +# IT4Innovations 2019 + +easyblock = 'PythonPackage' + +name = 'Meson' +version = '0.53.0' + +homepage = 'https://mesonbuild.com' +description = "Meson is a cross-platform build system designed to be both as fast and as user friendly as possible." + +toolchain = {'name': 'Py', 'version': '3.7'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Ninja', '1.9.0'), +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': 'mesonbuild'} + +sanity_check_paths = { + 'files': ['bin/meson'], + 'dirs': ['lib/python3.7/site-packages'], +} + +moduleclass = 'tools' diff --git a/n/Ninja/Ninja-1.9.0-Py-3.7.eb b/n/Ninja/Ninja-1.9.0-Py-3.7.eb new file mode 100644 index 00000000..a497606c --- /dev/null +++ b/n/Ninja/Ninja-1.9.0-Py-3.7.eb @@ -0,0 +1,26 @@ +# IT4Innovations 2020 + +easyblock = 'CmdCp' + +name = 'Ninja' +version = '1.9.0' + +homepage = 'https://ninja-build.org/' +description = "Ninja is a small build system with a focus on speed." + +toolchain = {'name': 'Py', 'version': '3.7'} + +source_urls = ['https://github.com/ninja-build/ninja/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['5d7ec75828f8d3fd1a0c2f31b5b0cea780cdfe1031359228c428c1a48bfcd5b9'] + +cmds_map = [('.*', "./configure.py --bootstrap")] + +files_to_copy = [(['ninja'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/ninja'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/n/numpy/numpy-1.18.1-Py-3.6.eb b/n/numpy/numpy-1.18.1-Py-3.6.eb index fe7566c7..709a15e5 100644 --- a/n/numpy/numpy-1.18.1-Py-3.6.eb +++ b/n/numpy/numpy-1.18.1-Py-3.6.eb @@ -8,7 +8,7 @@ version = '1.18.1' homepage = 'http://www.numpy.org' description = """NumPy is the fundamental package needed for scientific local_computing with Python.""" -toolchain = {'name': 'Py', 'version': '3.7'} +toolchain = {'name': 'Py', 'version': '3.6'} source_urls = ['https://github.com/numpy/numpy/releases/download/v%(version)s'] sources = [SOURCE_TAR_GZ] @@ -23,7 +23,7 @@ dependencies = [ ] sanity_check_paths = {'files': [], 'dirs': [ - 'lib/python3.7/site-packages/%(name)s-%(version)s-py3.7-linux-x86_64.egg/numpy'], } + 'lib/python3.6/site-packages/%(name)s-%(version)s-py3.6-linux-x86_64.egg/numpy'], } sanity_check_commands = [ ('python', '-c "import numpy; assert(numpy.__version__ == \'%(version)s\')"')] diff --git a/n/numpy/numpy-1.18.1-Py-3.7.eb b/n/numpy/numpy-1.18.1-Py-3.7.eb new file mode 100644 index 00000000..f7043e5e --- /dev/null +++ b/n/numpy/numpy-1.18.1-Py-3.7.eb @@ -0,0 +1,32 @@ +# IT4Innovations 2020 + +easyblock = 'PythonPackage' + +name = 'numpy' +version = '1.18.1' + +homepage = 'http://www.numpy.org' +description = """NumPy is the fundamental package needed for scientific local_computing with Python.""" + +toolchain = {'name': 'Py', 'version': '3.7'} + +source_urls = ['https://github.com/numpy/numpy/releases/download/v%(version)s'] +sources = [SOURCE_TAR_GZ] + +local_patch = [ + 'numpy-1.8.1-mkl.local_patch', + 'numpy-1.11.0-sse42.local_patch' +] + +dependencies = [ + ('mkl', '2019.5.281', '', True), + ('Cython', '0.29.14'), +] + +sanity_check_paths = {'files': [], 'dirs': [ + 'lib/python3.7/site-packages/%(name)s-%(version)s-py3.7-linux-x86_64.egg/numpy'], } + +sanity_check_commands = [ + ('python', '-c "import numpy; assert(numpy.__version__ == \'%(version)s\')"')] + +moduleclass = 'python' diff --git a/o/OpenBabel/OpenBabel-2.4.9-GCCcore-6.3.0-Python-3.7.3.eb b/o/OpenBabel/OpenBabel-2.4.9-GCCcore-6.3.0-Python-3.7.3.eb index 8d5d6d5e..a8890c7d 100644 --- a/o/OpenBabel/OpenBabel-2.4.9-GCCcore-6.3.0-Python-3.7.3.eb +++ b/o/OpenBabel/OpenBabel-2.4.9-GCCcore-6.3.0-Python-3.7.3.eb @@ -2,7 +2,7 @@ name = 'OpenBabel' version = '2.4.9' -versionsuffix = '-Python-%(local_pyver)s' +versionsuffix = '-Python-3.7.3' homepage = 'http://openbabel.org' description = """Open Babel is a chemical toolbox designed to speak the many diff --git a/o/OpenBabel/OpenBabel-3.0.0-Py-3.7.eb b/o/OpenBabel/OpenBabel-3.0.0-Py-3.7.eb new file mode 100644 index 00000000..a6b667ed --- /dev/null +++ b/o/OpenBabel/OpenBabel-3.0.0-Py-3.7.eb @@ -0,0 +1,39 @@ +# IT4Innovations 2019 + +name = 'OpenBabel' +version = '3.0.0' + +homepage = 'http://openbabel.org' +description = """Open Babel is a chemical toolbox designed to speak the many + languages of chemical data. It's an open, collaborative project allowing anyone + to search, convert, analyze, or store data from molecular modeling, chemistry, + solid-state materials, biochemistry, or related areas.""" + +toolchain = {'name': 'Py', 'version': '3.7'} +toolchainopts = {'optarch': True} + +source_urls = ['https://github.com/openbabel/openbabel/archive'] +sources = ['openbabel-3-0-0.tar.gz'] + +configopts = "-DPYTHON_BINDINGS=ON -DRUN_SWIG=ON" + +builddependencies = [ + ('CMake', '3.16.2', '', True) +] + +dependencies = [ + ('zlib', '1.2.11', '', True), + ('libxml2', '2.9.9', '', True), + ('Eigen', '3.3.7', '', True), + ('cairo', '1.17.2', '', True), + ('SWIG', '3.0.12'), +] + +#runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/obabel', 'lib/python3.7/site-packages/openbabel/openbabel.py'], + 'dirs': ['bin', 'include', 'lib'], +} + +moduleclass = 'chem' diff --git a/p/PCRE/PCRE-8.43.eb b/p/PCRE/PCRE-8.43.eb new file mode 100644 index 00000000..71e4d77d --- /dev/null +++ b/p/PCRE/PCRE-8.43.eb @@ -0,0 +1,20 @@ +# IT4Innovations 2020 + +easyblock = 'ConfigureMake' + +name = 'PCRE' +version = '8.43' + +homepage = 'http://www.pcre.org/' +description = """The PCRE library is a set of functions that implement regular expression pattern matching using + the same syntax and semantics as Perl 5.""" + +toolchain = SYSTEM +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic --disable-cpp --enable-utf --enable-unicode-properties" + +moduleclass = 'devel' diff --git a/p/Py/Py-3.7.eb b/p/Py/Py-3.7.eb index d7368986..de83b97b 100644 --- a/p/Py/Py-3.7.eb +++ b/p/Py/Py-3.7.eb @@ -1,4 +1,4 @@ -# IT4Innovations 2019 +# IT4Innovations 2020 easyblock = "Toolchain" @@ -6,13 +6,13 @@ name = 'Py' version = '3.7' homepage = 'https://www.python.org' -description = """Python 3.6 toolchain""" +description = """Python 3.7 toolchain""" toolchain = SYSTEM dependencies = [ - ('Python', '3.7.3', '-base', ('GCCcore', '6.3.0')), - ('GCC', '6.3.0-2.27'), + ('Python', '3.7.5', '-base', ('GCC', '8.3.0-2.32')), + ('GCC', '8.3.0-2.32'), ] moduleclass = 'toolchain' diff --git a/p/Python/Python-3.7.5-GCC-8.3.0-2.32-base.eb b/p/Python/Python-3.7.5-GCC-8.3.0-2.32-base.eb new file mode 100644 index 00000000..27d1a74f --- /dev/null +++ b/p/Python/Python-3.7.5-GCC-8.3.0-2.32-base.eb @@ -0,0 +1,62 @@ +# IT4Innovations 2020 + +name = 'Python' +version = '3.7.5' +versionsuffix = '-base' + +homepage = 'http://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'GCC', 'version': '8.3.0-2.32'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +dependencies = [ + ('bzip2', '1.0.8', '', True), # required for bz2 package in Python stdlib + ('zlib', '1.2.11', '', True), + ('libreadline', '8.0', '', True), + ('ncurses', '6.1', '', True), + ('SQLite', '3.30.1', '', True), + ('XZ', '5.2.4', '', True), + ('GMP', '6.1.2', '', True), # required for pycrypto + ('libffi', '3.3', '', True), # required for cryptography + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # Python 3.7 requires OpenSSL >= 1.0.2, uncomment line below if OS version is too old (e.g. CentOS 6) + # ('OpenSSL', '1.1.0j'), +] + +#osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# symlink 'pip' command to 'pip3' that is included with Python installation +# required so we can update pip to version included in extensions, using pip +installopts = " && ln -s %(installdir)s/bin/pip3 %(installdir)s/bin/pip" + +#exts_default_options = { +# 'download_dep_fail': True, +# 'use_pip': True, +#} + +# order is important! +# package versions updated Mar 15th 2019 +exts_list = [ + ('pip', '19.3.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + # don't use --ignore-installed, i.e. let pip remove older pip version included with Python + 'pip_ignore_installed': False, + }), + ('setuptools', '44.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools'], + 'source_tmpl': '%(name)s-%(version)s.zip', + # don't use --ignore-installed, i.e. let pip remove older setuptools version included with Python + 'pip_ignore_installed': False, + }), + ('wheel', '0.33.6', { + 'source_urls': ['https://pypi.python.org/packages/source/w/wheel'], + }) +] + +moduleclass = 'lang' diff --git a/p/phono3py/phono3py-1.18.2-Py-3.6.eb b/p/phono3py/phono3py-1.18.2-Py-3.6.eb deleted file mode 100644 index 5048c1b5..00000000 --- a/p/phono3py/phono3py-1.18.2-Py-3.6.eb +++ /dev/null @@ -1,25 +0,0 @@ -# IT4Innovations 2020 - -easyblock = "Conda" - -name = 'phono3py' -version = '1.18.2' - -homepage = 'http://phonopy.sourceforge.net/phono3py/index.html' -description = """This software calculates phonon-phonon interaction related properties""" - -toolchain = {'name': 'Py', 'version': '3.6'} - -requirements = "%(name)s=%(version)s" -channels = ['atztogo '] - -builddependencies = [ - ('Anaconda3', '2019.10', '', True), -] - -dependencies = [ - ('phonopy', '2.4.2'), - ('intel', '2019a', '', True), -] - -moduleclass = 'phys' diff --git a/p/phono3py/phono3py-1.18.2-conda.eb b/p/phono3py/phono3py-1.18.2-conda.eb new file mode 100644 index 00000000..090899f0 --- /dev/null +++ b/p/phono3py/phono3py-1.18.2-conda.eb @@ -0,0 +1,26 @@ +# IT4Innovations 2020 + +easyblock = "Conda" + +name = 'phono3py' +version = '1.18.2+1' +versionsuffix = '-conda' + +homepage = 'http://phonopy.sourceforge.net/phono3py/index.html' +description = """This software calculates phonon-phonon interaction related properties""" + +toolchain = SYSTEM + +dependencies = [ + ('Anaconda3', '2019.10'), +] + +requirements = "%(namelower)s=%(version)s python=3.7" +channels = ['atztogo'] + +sanity_check_paths = { + 'files': ['bin/phono3py', 'bin/phonopy'], + 'dirs': ['bin', 'lib'] +} + +moduleclass = 'phys' diff --git a/p/phonopy/phono3py-1.18.2-conda.eb b/p/phonopy/phono3py-1.18.2-conda.eb new file mode 100644 index 00000000..090899f0 --- /dev/null +++ b/p/phonopy/phono3py-1.18.2-conda.eb @@ -0,0 +1,26 @@ +# IT4Innovations 2020 + +easyblock = "Conda" + +name = 'phono3py' +version = '1.18.2+1' +versionsuffix = '-conda' + +homepage = 'http://phonopy.sourceforge.net/phono3py/index.html' +description = """This software calculates phonon-phonon interaction related properties""" + +toolchain = SYSTEM + +dependencies = [ + ('Anaconda3', '2019.10'), +] + +requirements = "%(namelower)s=%(version)s python=3.7" +channels = ['atztogo'] + +sanity_check_paths = { + 'files': ['bin/phono3py', 'bin/phonopy'], + 'dirs': ['bin', 'lib'] +} + +moduleclass = 'phys' diff --git a/p/phonopy/phonopy-2.4.2-conda.eb b/p/phonopy/phonopy-2.4.2-conda.eb new file mode 100644 index 00000000..d604cf69 --- /dev/null +++ b/p/phonopy/phonopy-2.4.2-conda.eb @@ -0,0 +1,26 @@ +# IT4Innovations 2020 + +easyblock = "Conda" + +name = 'phonopy' +version = '2.4.2' +versionsuffix = '-conda' + +homepage = 'http://phonopy.sourceforge.net/phono3py/index.html' +description = """This software calculates phonon-phonon interaction related properties""" + +toolchain = SYSTEM + +dependencies = [ + ('Anaconda3', '2019.10'), +] + +requirements = "%(namelower)s=%(version)s python=3.7" +channels = ['atztogo'] + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'lib'] +} + +moduleclass = 'phys' diff --git a/p/pixman/pixman-0.38.4.eb b/p/pixman/pixman-0.38.4.eb new file mode 100644 index 00000000..951743a1 --- /dev/null +++ b/p/pixman/pixman-0.38.4.eb @@ -0,0 +1,22 @@ +# IT4Innovations 2020 + +easyblock = 'ConfigureMake' + +name = 'pixman' +version = '0.38.4' + +homepage = 'http://www.pixman.org/' +description = """Pixman is a low-level software library for pixel manipulation, providing features such as image +local_compositing and trapezoid rasterization. Important users of pixman are the cairo graphics library and the X server.""" + +toolchain = SYSTEM + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['lib/libpixman-1.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/s/SQLite/SQLite-3.30.1.eb b/s/SQLite/SQLite-3.30.1.eb new file mode 100644 index 00000000..54919652 --- /dev/null +++ b/s/SQLite/SQLite-3.30.1.eb @@ -0,0 +1,39 @@ +# IT4Innovations 2020 + +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.30.1' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = SYSTEM + +source_urls = ['http://www.sqlite.org/2019/'] +local_version_minor_etc = version.split('.')[1:] +local_version_minor_etc += '0' * (3 - len(local_version_minor_etc)) +local_version_str = '%(version_major)s' + ''.join('%02d' % int(x) + for x in local_version_minor_etc) +sources = [ + 'sqlite-autoconf-%s.tar.gz' % local_version_str, + 'sqlite-amalgamation-%s.zip' % local_version_str, +] + +dependencies = [ + ('libreadline', '8.0'), + ('Tcl', '8.6.10'), +] + +sanity_check_paths = { + 'files': [ + 'bin/sqlite3', + 'include/sqlite3ext.h', + 'include/sqlite3.h', + 'lib/libsqlite3.a', + 'lib/libsqlite3.%s' % + SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'devel' diff --git a/s/SWIG/SWIG-3.0.12-Py-3.7.eb b/s/SWIG/SWIG-3.0.12-Py-3.7.eb new file mode 100644 index 00000000..0f9ab299 --- /dev/null +++ b/s/SWIG/SWIG-3.0.12-Py-3.7.eb @@ -0,0 +1,20 @@ +# IT4Innovations 2020 + +name = 'SWIG' +version = '3.0.12' + +homepage = 'http://www.swig.org/' +description = """SWIG is a software development tool that connects programs written in C and C++ with + a variety of high-level programming languages.""" + +toolchain = {'name': 'Py', 'version': '3.7'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('PCRE', '8.43', '', True), +] + +moduleclass = 'devel' diff --git a/s/SWIG/SWIG-4.0.1-Py-3.7.eb b/s/SWIG/SWIG-4.0.1-Py-3.7.eb new file mode 100644 index 00000000..f8d5f181 --- /dev/null +++ b/s/SWIG/SWIG-4.0.1-Py-3.7.eb @@ -0,0 +1,20 @@ +# IT4Innovations 2020 + +name = 'SWIG' +version = '4.0.1' + +homepage = 'http://www.swig.org/' +description = """SWIG is a software development tool that connects programs written in C and C++ with + a variety of high-level programming languages.""" + +toolchain = {'name': 'Py', 'version': '3.7'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('PCRE', '8.43', '', True), +] + +moduleclass = 'devel' diff --git a/t/Tcl/Tcl-8.6.10.eb b/t/Tcl/Tcl-8.6.10.eb new file mode 100644 index 00000000..81a264e0 --- /dev/null +++ b/t/Tcl/Tcl-8.6.10.eb @@ -0,0 +1,27 @@ +# IT4Innovations 2019 +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.10' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, +testing and many more.""" + +toolchain = SYSTEM + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('zlib', '1.2.11'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' diff --git a/u/util-linux/util-linux-2.34.eb b/u/util-linux/util-linux-2.34.eb new file mode 100644 index 00000000..23421b5a --- /dev/null +++ b/u/util-linux/util-linux-2.34.eb @@ -0,0 +1,45 @@ +# IT4Innovations 2020 + +easyblock = 'ConfigureMake' + +name = 'util-linux' +version = '2.34' + +homepage = 'http://www.kernel.org/pub/linux/utils/util-linux' + +description = "Set of Linux utilities" + +toolchain = SYSTEM +toolchainopts = {'pic': True} + +source_urls = ['%s/v%%(version_major_minor)s' % homepage] +sources = [SOURCELOWER_TAR_GZ] + +# disable account related utilities (they need OS dependent pam-devel files) +# disable wall and friends (requires group changing permissions for install user) +# install systemd service files in install dir +# install bash completion files in install dir +configopts = "--disable-chfn-chsh --disable-login --disable-su --disable-rfkill " +configopts += "--disable-wall --disable-use-tty-group " +configopts += "--disable-makeinstall-chown --disable-makeinstall-setuid " +configopts += "--with-systemdsystemunitdir='${prefix}/systemd' " +configopts += "--with-bashcompletiondir='${prefix}/share/bash-completion/completions' " +# disable building Python bindings (since we don't include Python as a dep) +configopts += "--without-python " + + +builddependencies = [ + ('binutils', '2.27'), +] + +dependencies = [ + ('ncurses', '6.1'), + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ['lib/lib%s.a' % x for x in ['blkid', 'mount', 'uuid']], + 'dirs': ['include', 'bin', 'share', 'sbin'], +} + +moduleclass = 'tools'