Merge branch 'develop' of https://github.com/easybuilders/easybuild-e…

…asyconfigs into 20210224165738_new_pr_OpenCV451
easybuilders · Feb 25, 2021 · aaf4d63 · aaf4d63
2 parents 1eab0e6 + 65b0d3a
commit aaf4d63
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diff --git a/easybuild/easyconfigs/a/ABySS/ABySS-2.2.5-foss-2020b.eb b/easybuild/easyconfigs/a/ABySS/ABySS-2.2.5-foss-2020b.eb
@@ -0,0 +1,29 @@
+easyblock = 'ConfigureMake'
+
+name = 'ABySS'
+version = '2.2.5'
+
+homepage = 'https://www.bcgsc.ca/platform/bioinfo/software/abyss'
+description = """Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler"""
+
+toolchain = {'name': 'foss', 'version': '2020b'}
+toolchainopts = {'usempi': True}
+
+source_urls = ['http://github.com/bcgsc/abyss/releases/download/%(version)s/']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['38e886f455074c76b32dd549e94cc345f46cb1d33ab11ad3e8e1f5214fc65521']
+
+dependencies = [
+    ('Boost', '1.74.0'),
+    ('sparsehash', '2.0.4'),
+    ('SQLite', '3.33.0'),
+]
+
+configopts = 'CXXFLAGS="$CXXFLAGS -Wno-error=deprecated-copy"'
+
+sanity_check_paths = {
+    'files': ["bin/ABYSS", "bin/ABYSS-P"],
+    'dirs': []
+}
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-8.2.0-2.31.1-Perl-5.28.1.eb b/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-8.2.0-2.31.1-Perl-5.28.1.eb
@@ -21,6 +21,8 @@ dependencies = [
     ('HTSlib', '1.9'),
 ]
 
+preconfigopts = "env HTSLIB_DIR=$EBROOTHTSLIB"
+
 options = {'modulename': 'Bio::DB::HTS'}
 
 sanity_check_paths = {

diff --git a/easybuild/easyconfigs/b/Blosc/Blosc-1.21.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/Blosc/Blosc-1.21.0-GCCcore-10.2.0.eb
@@ -0,0 +1,28 @@
+easyblock = 'CMakeMake'
+
+name = 'Blosc'
+version = '1.21.0'
+
+homepage = 'https://www.blosc.org/'
+
+description = "Blosc, an extremely fast, multi-threaded, meta-compressor library"
+
+toolchain = {'name': 'GCCcore', 'version': '10.2.0'}
+toolchainopts = {'pic': True, 'cstd': 'c++11'}
+
+source_urls = ['https://github.com/Blosc/c-blosc/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['b0ef4fda82a1d9cbd11e0f4b9685abf14372db51703c595ecd4d76001a8b342d']
+
+builddependencies = [
+    ('binutils', '2.35'),
+    ('CMake', '3.18.4'),
+]
+
+sanity_check_paths = {
+    'files': ['include/blosc-export.h', 'include/blosc.h', 'lib/libblosc.a',
+              'lib/libblosc.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-foss-2020b.eb b/easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-foss-2020b.eb
@@ -0,0 +1,41 @@
+easyblock = 'PythonBundle'
+
+name = 'bokeh'
+version = '2.2.3'
+
+homepage = 'https://github.com/bokeh/bokeh'
+description = "Statistical and novel interactive HTML plots for Python"
+
+toolchain = {'name': 'foss', 'version': '2020b'}
+
+dependencies = [
+    ('Python', '3.8.6'),
+    ('PyYAML', '5.3.1'),
+    ('Pillow', '8.0.1'),
+    ('SciPy-bundle', '2020.11'),
+    ('typing-extensions', '3.7.4.3'),
+]
+
+use_pip = True
+
+exts_default_options = {'source_urls': [PYPI_SOURCE]}
+
+exts_list = [
+    ('tornado', '6.1', {
+        'checksums': ['33c6e81d7bd55b468d2e793517c909b139960b6c790a60b7991b9b6b76fb9791'],
+    }),
+    (name, version, {
+        'checksums': ['c4a3f97afe5f525019dd58ee8c4e3d43f53fe1b1ac264ccaae9b02c07b2abc17'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/bokeh'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ["bokeh --help"]
+
+sanity_pip_check = True
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-intel-2020b.eb b/easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-intel-2020b.eb
@@ -0,0 +1,41 @@
+easyblock = 'PythonBundle'
+
+name = 'bokeh'
+version = '2.2.3'
+
+homepage = 'https://github.com/bokeh/bokeh'
+description = "Statistical and novel interactive HTML plots for Python"
+
+toolchain = {'name': 'intel', 'version': '2020b'}
+
+dependencies = [
+    ('Python', '3.8.6'),
+    ('PyYAML', '5.3.1'),
+    ('Pillow', '8.0.1'),
+    ('SciPy-bundle', '2020.11'),
+    ('typing-extensions', '3.7.4.3'),
+]
+
+use_pip = True
+
+exts_default_options = {'source_urls': [PYPI_SOURCE]}
+
+exts_list = [
+    ('tornado', '6.1', {
+        'checksums': ['33c6e81d7bd55b468d2e793517c909b139960b6c790a60b7991b9b6b76fb9791'],
+    }),
+    (name, version, {
+        'checksums': ['c4a3f97afe5f525019dd58ee8c4e3d43f53fe1b1ac264ccaae9b02c07b2abc17'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/bokeh'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ["bokeh --help"]
+
+sanity_pip_check = True
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/c/Clang/Clang-11.0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/Clang/Clang-11.0.1-GCCcore-10.2.0.eb
@@ -0,0 +1,71 @@
+##
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+#
+# Copyright:: Copyright 2013-2015 Dmitri Gribenko, Ward Poelmans
+# Authors:: Dmitri Gribenko <gribozavr@gmail.com>
+# Authors:: Ward Poelmans <wpoely86@gmail.com>
+# License:: GPLv2 or later, MIT, three-clause BSD.
+# $Id$
+##
+
+name = 'Clang'
+version = '11.0.1'
+
+homepage = 'https://clang.llvm.org/'
+description = """C, C++, Objective-C compiler, based on LLVM.  Does not
+ include C++ standard library -- use libstdc++ from GCC."""
+
+# Clang also depends on libstdc++ during runtime, but this dependency is
+# already specified as the toolchain.
+toolchain = {'name': 'GCCcore', 'version': '10.2.0'}
+
+source_urls = ["https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s"]
+sources = [
+    'llvm-%(version)s.src.tar.xz',
+    'clang-%(version)s.src.tar.xz',
+    'compiler-rt-%(version)s.src.tar.xz',
+    'polly-%(version)s.src.tar.xz',
+    'openmp-%(version)s.src.tar.xz',
+    # Also include the LLVM linker
+    'lld-%(version)s.src.tar.xz',
+    'libcxx-%(version)s.src.tar.xz',
+    'libcxxabi-%(version)s.src.tar.xz',
+    'clang-tools-extra-%(version)s.src.tar.xz',
+]
+checksums = [
+    'ccd87c254b6aebc5077e4e6977d08d4be888e7eb672c6630a26a15d58b59b528',  # llvm-11.0.1.src.tar.xz
+    '73f572c2eefc5a155e01bcd84815751d722a4d3925f53c144acfb93eeb274b4d',  # clang-11.0.1.src.tar.xz
+    '087be3f1116e861cd969c9b0b0903c27028b52eaf45157276f50a9c2500687fc',  # compiler-rt-11.0.1.src.tar.xz
+    '08dfce0e7b168d621f6c64b6b60a25300acb9337345ab0014c4f64a053c5b9ea',  # polly-11.0.1.src.tar.xz
+    '4d15a21b90e7de2f01296503f6e4b16c50197fbe9c82e7e81f9c07e28bd82ca7',  # openmp-11.0.1.src.tar.xz
+    '60ba0da01a391078dcc437fee629f3bf7e30e06467a3a060b4a2a3aa661308b7',  # lld-11.0.1.src.tar.xz
+    '9fd5f669621ffea88a2b93e3d99f3a958b5defb954f71bf754709b63275f5e3d',  # libcxx-11.0.1.src.tar.xz
+    '4a697056a5c08621a8380dcaf3836525835aa76b3008d9e8f27abf9270bf683f',  # libcxxabi-11.0.1.src.tar.xz
+    '2ca211dd8cc396a919709a9bc35af11b7d425df0c608d85ba6629242893516c9',  # clang-tools-extra-11.0.1.src.tar.xz
+]
+
+dependencies = [
+    # since Clang is a compiler, binutils is a runtime dependency too
+    ('binutils', '2.35'),
+    ('hwloc', '2.2.0'),
+    ('libxml2', '2.9.10'),
+    ('ncurses', '6.2'),
+    ('GMP', '6.2.0'),
+    ('Z3', '4.8.10'),
+]
+
+builddependencies = [
+    ('CMake', '3.18.4'),
+    ('Python', '3.8.6'),
+]
+
+assertions = True
+usepolly = True
+build_lld = True
+libcxx = True
+enable_rtti = True
+build_extra_clang_tools = True
+
+skip_all_tests = True
+
+moduleclass = 'compiler'
diff --git a/easybuild/easyconfigs/d/dask/dask-2021.2.0-foss-2020b.eb b/easybuild/easyconfigs/d/dask/dask-2021.2.0-foss-2020b.eb
@@ -0,0 +1,77 @@
+easyblock = 'PythonBundle'
+
+name = 'dask'
+version = '2021.2.0'
+
+homepage = 'https://dask.org/'
+description = """Dask natively scales Python. Dask provides advanced parallelism for analytics, enabling performance
+ at scale for the tools you love."""
+
+toolchain = {'name': 'foss', 'version': '2020b'}
+
+dependencies = [
+    ('Python', '3.8.6'),
+    ('PyYAML', '5.3.1'),
+    ('SciPy-bundle', '2020.11'),
+    ('bokeh', '2.2.3'),
+]
+
+use_pip = True
+
+exts_default_options = {'source_urls': [PYPI_SOURCE]}
+
+exts_list = [
+    ('fsspec', '0.8.7', {
+        'checksums': ['4b11557a90ac637089b10afa4c77adf42080c0696f6f2771c41ce92d73c41432'],
+    }),
+    ('toolz', '0.11.1', {
+        'checksums': ['c7a47921f07822fe534fb1c01c9931ab335a4390c782bd28c6bcc7c2f71f3fbf'],
+    }),
+    ('locket', '0.2.1', {
+        'checksums': ['3e1faba403619fe201552f083f1ecbf23f550941bc51985ac6ed4d02d25056dd'],
+    }),
+    ('partd', '1.1.0', {
+        'checksums': ['6e258bf0810701407ad1410d63d1a15cfd7b773fd9efe555dac6bb82cc8832b0'],
+    }),
+    ('HeapDict', '1.0.1', {
+        'checksums': ['8495f57b3e03d8e46d5f1b2cc62ca881aca392fd5cc048dc0aa2e1a6d23ecdb6'],
+    }),
+    ('zict', '2.0.0', {
+        'checksums': ['8e2969797627c8a663575c2fc6fcb53a05e37cdb83ee65f341fc6e0c3d0ced16'],
+    }),
+    ('tblib', '1.7.0', {
+        'checksums': ['059bd77306ea7b419d4f76016aef6d7027cc8a0785579b5aad198803435f882c'],
+    }),
+    ('msgpack', '1.0.2', {
+        'checksums': ['fae04496f5bc150eefad4e9571d1a76c55d021325dcd484ce45065ebbdd00984'],
+    }),
+    ('cloudpickle', '1.6.0', {
+        'checksums': ['9bc994f9e9447593bd0a45371f0e7ac7333710fcf64a4eb9834bf149f4ef2f32'],
+    }),
+    (name, version, {
+        'checksums': ['e7054b8d685205e95c789900ae87d6174550180cbe38a3cb1142e10c73004c22'],
+    }),
+    ('distributed', version, {
+        'checksums': ['9150b99b2c28e7c238c486b117154abd545c6990080d084aaff02f803f86f75e'],
+    }),
+    ('dask-mpi', '2.21.0', {
+        'checksums': ['76e153fc8c58047d898970b33ede0ab1990bd4e69cc130c6627a96f11b12a1a7'],
+    }),
+    ('docrep', '0.3.2', {
+        'checksums': ['ed8a17e201abd829ef8da78a0b6f4d51fb99a4cbd0554adbed3309297f964314'],
+    }),
+    ('dask-jobqueue', '0.7.2', {
+        'checksums': ['1767f4146b2663d9d2eaef62b882a86e1df0bccdb8ae68ae3e5e546aa6796d35'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/dask-%s' % x for x in ['mpi', 'scheduler', 'ssh', 'worker']],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ["dask-scheduler --help"]
+
+sanity_pip_check = True
+
+moduleclass = 'data'
diff --git a/easybuild/easyconfigs/d/dask/dask-2021.2.0-intel-2020b.eb b/easybuild/easyconfigs/d/dask/dask-2021.2.0-intel-2020b.eb
@@ -0,0 +1,77 @@
+easyblock = 'PythonBundle'
+
+name = 'dask'
+version = '2021.2.0'
+
+homepage = 'https://dask.org/'
+description = """Dask natively scales Python. Dask provides advanced parallelism for analytics, enabling performance
+ at scale for the tools you love."""
+
+toolchain = {'name': 'intel', 'version': '2020b'}
+
+dependencies = [
+    ('Python', '3.8.6'),
+    ('PyYAML', '5.3.1'),
+    ('SciPy-bundle', '2020.11'),
+    ('bokeh', '2.2.3'),
+]
+
+use_pip = True
+
+exts_default_options = {'source_urls': [PYPI_SOURCE]}
+
+exts_list = [
+    ('fsspec', '0.8.7', {
+        'checksums': ['4b11557a90ac637089b10afa4c77adf42080c0696f6f2771c41ce92d73c41432'],
+    }),
+    ('toolz', '0.11.1', {
+        'checksums': ['c7a47921f07822fe534fb1c01c9931ab335a4390c782bd28c6bcc7c2f71f3fbf'],
+    }),
+    ('locket', '0.2.1', {
+        'checksums': ['3e1faba403619fe201552f083f1ecbf23f550941bc51985ac6ed4d02d25056dd'],
+    }),
+    ('partd', '1.1.0', {
+        'checksums': ['6e258bf0810701407ad1410d63d1a15cfd7b773fd9efe555dac6bb82cc8832b0'],
+    }),
+    ('HeapDict', '1.0.1', {
+        'checksums': ['8495f57b3e03d8e46d5f1b2cc62ca881aca392fd5cc048dc0aa2e1a6d23ecdb6'],
+    }),
+    ('zict', '2.0.0', {
+        'checksums': ['8e2969797627c8a663575c2fc6fcb53a05e37cdb83ee65f341fc6e0c3d0ced16'],
+    }),
+    ('tblib', '1.7.0', {
+        'checksums': ['059bd77306ea7b419d4f76016aef6d7027cc8a0785579b5aad198803435f882c'],
+    }),
+    ('msgpack', '1.0.2', {
+        'checksums': ['fae04496f5bc150eefad4e9571d1a76c55d021325dcd484ce45065ebbdd00984'],
+    }),
+    ('cloudpickle', '1.6.0', {
+        'checksums': ['9bc994f9e9447593bd0a45371f0e7ac7333710fcf64a4eb9834bf149f4ef2f32'],
+    }),
+    (name, version, {
+        'checksums': ['e7054b8d685205e95c789900ae87d6174550180cbe38a3cb1142e10c73004c22'],
+    }),
+    ('distributed', version, {
+        'checksums': ['9150b99b2c28e7c238c486b117154abd545c6990080d084aaff02f803f86f75e'],
+    }),
+    ('dask-mpi', '2.21.0', {
+        'checksums': ['76e153fc8c58047d898970b33ede0ab1990bd4e69cc130c6627a96f11b12a1a7'],
+    }),
+    ('docrep', '0.3.2', {
+        'checksums': ['ed8a17e201abd829ef8da78a0b6f4d51fb99a4cbd0554adbed3309297f964314'],
+    }),
+    ('dask-jobqueue', '0.7.2', {
+        'checksums': ['1767f4146b2663d9d2eaef62b882a86e1df0bccdb8ae68ae3e5e546aa6796d35'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/dask-%s' % x for x in ['mpi', 'scheduler', 'ssh', 'worker']],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ["dask-scheduler --help"]
+
+sanity_pip_check = True
+
+moduleclass = 'data'
diff --git a/...uild/easyconfigs/e/EnsEMBLCoreAPI/EnsEMBLCoreAPI-96.0-r20190601-foss-2019a-Perl-5.28.1.eb b/...uild/easyconfigs/e/EnsEMBLCoreAPI/EnsEMBLCoreAPI-96.0-r20190601-foss-2019a-Perl-5.28.1.eb
@@ -169,7 +169,6 @@ sanity_check_paths = {
 modextrapaths = {
     'PERL5LIB': ['ensembl/modules', 'ensembl-compara/modules', 'ensembl-funcgen/modules',
                  'ensembl-variation/modules', 'ensembl-io/modules', 'lib/perl5/site_perl/%(perlver)s/'],
-    'HTSLIB_DIR': "$EBROOTHTSLIB/include",
 }
 
 moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/e/ecCodes/ecCodes-2.20.0-gompi-2020b.eb b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.20.0-gompi-2020b.eb
@@ -19,7 +19,7 @@ builddependencies = [('CMake', '3.18.4')]
 
 dependencies = [
     ('netCDF', '4.7.4'),
-    ('JasPer', '2.0.14'),
+    ('JasPer', '2.0.24'),
     ('libjpeg-turbo', '2.0.5'),
     ('libpng', '1.6.37'),
     ('zlib', '1.2.11'),