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Original file line number Diff line number Diff line change
Expand Up @@ -16,10 +16,10 @@ checksums = [
'05090efb306fc84d09f007a848ce0d0472f8633633b0a6eaf86ab075d092bc0d', # ABRA2-2.22_fix-Makefile.patch
]

builddependencies = [('Maven', '3.6.3', '', True)]
builddependencies = [('Maven', '3.6.3', '', SYSTEM)]

dependencies = [
('Java', '11', '', True),
('Java', '11', '', SYSTEM),
('BWA', '0.7.17'),
]

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4 changes: 2 additions & 2 deletions easybuild/easyconfigs/a/ABRA2/ABRA2-2.23-GCC-10.2.0.eb
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Expand Up @@ -16,10 +16,10 @@ checksums = [
'05090efb306fc84d09f007a848ce0d0472f8633633b0a6eaf86ab075d092bc0d', # ABRA2-2.22_fix-Makefile.patch
]

builddependencies = [('Maven', '3.6.3', '', True)]
builddependencies = [('Maven', '3.6.3', '', SYSTEM)]

dependencies = [
('Java', '11', '', True),
('Java', '11', '', SYSTEM),
('BWA', '0.7.17'),
]

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4 changes: 2 additions & 2 deletions easybuild/easyconfigs/a/ABRA2/ABRA2-2.23-GCC-9.3.0.eb
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Expand Up @@ -16,10 +16,10 @@ checksums = [
'05090efb306fc84d09f007a848ce0d0472f8633633b0a6eaf86ab075d092bc0d', # ABRA2-2.22_fix-Makefile.patch
]

builddependencies = [('Maven', '3.6.3', '', True)]
builddependencies = [('Maven', '3.6.3', '', SYSTEM)]

dependencies = [
('Java', '11', '', True),
('Java', '11', '', SYSTEM),
('BWA', '0.7.17'),
]

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Expand Up @@ -21,7 +21,7 @@ checksums = ['2d361fcc2b800c3daaf25692988af6105669cba2ff513aba82f36089beb2839f']

dependencies = [
('Perl', '5.32.0'),
('Java', '13', '', True),
('Java', '13', '', SYSTEM),
('BioPerl', '1.7.8'),
('HMMER', '3.3.2'),
('EMBOSS', '6.6.0', local_javasuffix),
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Expand Up @@ -21,7 +21,7 @@ checksums = [
]

builddependencies = [('binutils', '2.35')]
dependencies = [('Java', '11', '', True)]
dependencies = [('Java', '11', '', SYSTEM)]

configopts = '--disable-examples --disable-csharp --disable-python'

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Expand Up @@ -21,7 +21,7 @@ checksums = [
]

builddependencies = [('binutils', '2.36.1')]
dependencies = [('Java', '11', '', True)]
dependencies = [('Java', '11', '', SYSTEM)]

configopts = '--disable-examples --disable-csharp --disable-python'

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Expand Up @@ -22,7 +22,7 @@ checksums = [

builddependencies = [('binutils', '2.37')]

dependencies = [('Java', '11', '', True)]
dependencies = [('Java', '11', '', SYSTEM)]

configopts = '--disable-examples --disable-csharp --disable-python'

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Expand Up @@ -22,7 +22,7 @@ checksums = [

builddependencies = [('binutils', '2.38')]

dependencies = [('Java', '11', '', True)]
dependencies = [('Java', '11', '', SYSTEM)]

configopts = '--disable-examples --disable-csharp --disable-python'

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2 changes: 1 addition & 1 deletion easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-7.3.0.eb
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Expand Up @@ -20,7 +20,7 @@ checksums = [
]

builddependencies = [('binutils', '2.30')]
dependencies = [('Java', '1.8', '', True)]
dependencies = [('Java', '1.8', '', SYSTEM)]

configopts = '--disable-examples --disable-csharp --disable-python'

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2 changes: 1 addition & 1 deletion easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-8.2.0.eb
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Expand Up @@ -20,7 +20,7 @@ checksums = [
]

builddependencies = [('binutils', '2.31.1')]
dependencies = [('Java', '1.8', '', True)]
dependencies = [('Java', '1.8', '', SYSTEM)]

configopts = '--disable-examples --disable-csharp --disable-python'

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Expand Up @@ -21,7 +21,7 @@ checksums = [
]

builddependencies = [('binutils', '2.32')]
dependencies = [('Java', '11', '', True)]
dependencies = [('Java', '11', '', SYSTEM)]

configopts = '--disable-examples --disable-csharp --disable-python'

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Expand Up @@ -21,7 +21,7 @@ checksums = [
]

builddependencies = [('binutils', '2.34')]
dependencies = [('Java', '11', '', True)]
dependencies = [('Java', '11', '', SYSTEM)]

configopts = '--disable-examples --disable-csharp --disable-python'

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2 changes: 1 addition & 1 deletion easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2017b.eb
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Expand Up @@ -19,7 +19,7 @@ checksums = [
'd167d3248a03301bc93efcb37d5df959aae6794968e42231af0b0dd26d6a2e66', # ANTLR-2.7.7_includes.patch
]

dependencies = [('Java', '1.8.0_152', '', True)]
dependencies = [('Java', '1.8.0_152', '', SYSTEM)]

configopts = '--disable-examples --disable-csharp --disable-python'

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Expand Up @@ -21,7 +21,7 @@ checksums = [
]

dependencies = [
('Java', '1.8.0_162', '', True),
('Java', '1.8.0_162', '', SYSTEM),
('Python', '2.7.14'),
]

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2 changes: 1 addition & 1 deletion easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2018b.eb
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Expand Up @@ -19,7 +19,7 @@ checksums = [
'd167d3248a03301bc93efcb37d5df959aae6794968e42231af0b0dd26d6a2e66', # ANTLR-2.7.7_includes.patch
]

dependencies = [('Java', '1.8', '', True)]
dependencies = [('Java', '1.8', '', SYSTEM)]

configopts = '--disable-examples --disable-csharp --disable-python'

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2 changes: 1 addition & 1 deletion easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2019a.eb
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Expand Up @@ -20,7 +20,7 @@ checksums = [
]

builddependencies = [('binutils', '2.31.1')]
dependencies = [('Java', '11', '', True)]
dependencies = [('Java', '11', '', SYSTEM)]

configopts = '--disable-examples --disable-csharp --disable-python'

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Expand Up @@ -21,7 +21,7 @@ checksums = [
]

dependencies = [
('Java', '1.8.0_152', '', True),
('Java', '1.8.0_152', '', SYSTEM),
('Python', '2.7.14'),
]

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2 changes: 1 addition & 1 deletion easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2017b.eb
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Expand Up @@ -19,7 +19,7 @@ checksums = [
'd167d3248a03301bc93efcb37d5df959aae6794968e42231af0b0dd26d6a2e66', # ANTLR-2.7.7_includes.patch
]

dependencies = [('Java', '1.8.0_152', '', True)]
dependencies = [('Java', '1.8.0_152', '', SYSTEM)]

configopts = '--disable-examples --disable-csharp --disable-python'

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Expand Up @@ -21,7 +21,7 @@ checksums = [
]

dependencies = [
('Java', '1.8.0_162', '', True),
('Java', '1.8.0_162', '', SYSTEM),
('Python', '3.6.4'),
]

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Expand Up @@ -29,7 +29,7 @@ builddependencies = [
]

dependencies = [
('CUDA', '11.3.1', '', True),
('CUDA', '11.3.1', '', SYSTEM),
('Boost', '1.76.0'),
('Python', '3.9.5'),
('OpenCV', '4.5.3', '-CUDA-%(cudaver)s-contrib'),
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2 changes: 1 addition & 1 deletion easybuild/easyconfigs/a/ASTRID/ASTRID-2.2.1-gompi-2019a.eb
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Expand Up @@ -18,7 +18,7 @@ checksums = [
]

dependencies = [
('Java', '11', '', True),
('Java', '11', '', SYSTEM),
('phylokit', '1.0'),
('Boost', '1.70.0'),
]
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Expand Up @@ -17,7 +17,7 @@ builddependencies = [

dependencies = [
('Python', '3.9.5'),
('CUDA', '11.3.1', '', True),
('CUDA', '11.3.1', '', SYSTEM),
('SciPy-bundle', '2021.05'),
('PyYAML', '5.4.1'),
('TensorFlow', '2.6.0', versionsuffix),
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@ builddependencies = [

dependencies = [
('Python', '3.9.5'),
('CUDA', '11.3.1', '', True),
('CUDA', '11.3.1', '', SYSTEM),
('SciPy-bundle', '2021.05'),
('PyYAML', '5.4.1'),
('TensorFlow', '2.6.0', versionsuffix),
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Expand Up @@ -42,7 +42,7 @@ dependencies = [
('bzip2', '1.0.8'),
('libreadline', '8.0'),
('matplotlib', '3.2.1', '-Python-%(pyver)s'),
('NCCL', '2.8.3', '-CUDA-%(cudaver)s', True),
('NCCL', '2.8.3', '-CUDA-%(cudaver)s', SYSTEM),
('netCDF-Fortran', '4.5.2'),
('netCDF', '4.7.4'),
('Perl', '5.30.2'),
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Expand Up @@ -53,7 +53,7 @@ dependencies = [
('PnetCDF', '1.12.2'),
('Tkinter', '3.8.6'),
('X11', '20201008'),
('NCCL', '2.8.3', '-CUDA-%(cudaver)s', True),
('NCCL', '2.8.3', '-CUDA-%(cudaver)s', SYSTEM),
]

# Some CUDA tests differs from expected results
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Expand Up @@ -32,11 +32,11 @@ sources = [{
checksums = ['04af67517b752e15b5add27f4584f8c11293a0ed1353d3c1dd60c3c6e2dcb329']

dependencies = [
('Java', '11', '', True),
('Java', '11', '', SYSTEM),
('BWA', '0.7.17'),
('Trimmomatic', '0.39', '-Java-%(javashortver)s', True),
('Trimmomatic', '0.39', '-Java-%(javashortver)s', SYSTEM),
('SAMtools', '1.10'),
('Nextflow', '19.12.0', '', True),
('Nextflow', '19.12.0', '', SYSTEM),
]

local_exe_files = [
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Expand Up @@ -29,7 +29,7 @@ builddependencies = [

dependencies = [
('Boost', '1.67.0'),
('CUDA', local_cudaver, '', True),
('CUDA', local_cudaver, '', SYSTEM),
]

separate_build_dir = True
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Expand Up @@ -21,7 +21,7 @@ sources = ['v%(version)s.tar.gz']
checksums = ['6557df95eed99323befddcef6b8da8b67eba22476efccd1e69a87ffdf075e5f4']

dependencies = [
('CUDA', '11.3.1', '', True),
('CUDA', '11.3.1', '', SYSTEM),
]

parallel = 1
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Expand Up @@ -19,7 +19,7 @@ checksums = ['954bd69b391edc12d6a4a51a2dd1476543da5c6bbf05a95b59dc0dd6fd4c2969']
dependencies = [('M4', '1.4.17')]

# use same binutils version that was used when building GCCcore toolchain
builddependencies = [('binutils', '2.25', '', True)]
builddependencies = [('binutils', '2.25', '', SYSTEM)]

sanity_check_paths = {
'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", "autoscan",
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Expand Up @@ -19,7 +19,7 @@ checksums = ['954bd69b391edc12d6a4a51a2dd1476543da5c6bbf05a95b59dc0dd6fd4c2969']
dependencies = [('M4', '1.4.18')]

# use same binutils version that was used when building GCCcore toolchain
builddependencies = [('binutils', '2.26', '', True)]
builddependencies = [('binutils', '2.26', '', SYSTEM)]

sanity_check_paths = {
'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", "autoscan",
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Expand Up @@ -19,7 +19,7 @@ checksums = ['954bd69b391edc12d6a4a51a2dd1476543da5c6bbf05a95b59dc0dd6fd4c2969']
dependencies = [('M4', '1.4.18')]

# use same binutils version that was used when building GCCcore toolchain
builddependencies = [('binutils', '2.26', '', True)]
builddependencies = [('binutils', '2.26', '', SYSTEM)]

sanity_check_paths = {
'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", "autoscan",
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Expand Up @@ -19,7 +19,7 @@ checksums = ['954bd69b391edc12d6a4a51a2dd1476543da5c6bbf05a95b59dc0dd6fd4c2969']
dependencies = [('M4', '1.4.17')]

# use same binutils version that was used when building GCCcore toolchain
builddependencies = [('binutils', '2.27', '', True)]
builddependencies = [('binutils', '2.27', '', SYSTEM)]

sanity_check_paths = {
'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", "autoscan",
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Expand Up @@ -19,7 +19,7 @@ checksums = ['954bd69b391edc12d6a4a51a2dd1476543da5c6bbf05a95b59dc0dd6fd4c2969']
dependencies = [('M4', '1.4.17')]

# use same binutils version that was used when building GCCcore toolchain
builddependencies = [('binutils', '2.27', '', True)]
builddependencies = [('binutils', '2.27', '', SYSTEM)]

sanity_check_paths = {
'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", "autoscan",
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Expand Up @@ -19,7 +19,7 @@ checksums = ['954bd69b391edc12d6a4a51a2dd1476543da5c6bbf05a95b59dc0dd6fd4c2969']
dependencies = [('M4', '1.4.18')]

# use same binutils version that was used when building GCCcore toolchain
builddependencies = [('binutils', '2.27', '', True)]
builddependencies = [('binutils', '2.27', '', SYSTEM)]

sanity_check_paths = {
'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", "autoscan",
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Expand Up @@ -31,7 +31,7 @@ checksums = [
dependencies = [('Autoconf', '2.69')]

# use same binutils version that was used when building GCCcore toolchain
builddependencies = [('binutils', '2.25', '', True)]
builddependencies = [('binutils', '2.25', '', SYSTEM)]

sanity_check_paths = {
'files': ['bin/automake', 'bin/aclocal'],
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Expand Up @@ -31,7 +31,7 @@ checksums = [
dependencies = [('Autoconf', '2.69')]

# use same binutils version that was used when building GCCcore toolchain
builddependencies = [('binutils', '2.26', '', True)]
builddependencies = [('binutils', '2.26', '', SYSTEM)]

sanity_check_paths = {
'files': ['bin/automake', 'bin/aclocal'],
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Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,7 @@ checksums = [
dependencies = [('Autoconf', '2.69')]

# use same binutils version that was used when building GCCcore toolchain
builddependencies = [('binutils', '2.26', '', True)]
builddependencies = [('binutils', '2.26', '', SYSTEM)]

sanity_check_paths = {
'files': ['bin/automake', 'bin/aclocal'],
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Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,7 @@ checksums = [
dependencies = [('Autoconf', '2.69')]

# use same binutils version that was used when building GCCcore toolchain
builddependencies = [('binutils', '2.27', '', True)]
builddependencies = [('binutils', '2.27', '', SYSTEM)]

sanity_check_paths = {
'files': ['bin/automake', 'bin/aclocal'],
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Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,7 @@ checksums = [
dependencies = [('Autoconf', '2.69')]

# use same binutils version that was used when building GCCcore toolchain
builddependencies = [('binutils', '2.27', '', True)]
builddependencies = [('binutils', '2.27', '', SYSTEM)]

sanity_check_paths = {
'files': ['bin/automake', 'bin/aclocal'],
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Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,7 @@ checksums = [
dependencies = [('Autoconf', '2.69')]

# use same binutils version that was used when building GCCcore toolchain
builddependencies = [('binutils', '2.27', '', True)]
builddependencies = [('binutils', '2.27', '', SYSTEM)]

sanity_check_paths = {
'files': ['bin/automake', 'bin/aclocal'],
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2 changes: 1 addition & 1 deletion easybuild/easyconfigs/a/ant/ant-1.10.1-Java-1.8.eb
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Expand Up @@ -17,7 +17,7 @@ sources = ['apache-%(name)s-%(version)s-src.tar.gz']
checksums = ['68f7ced0aa15d1f9f672f23d67c86deaf728e9576936313cfbff4f7a0e6ce382']

# specify dependency on Java/1.8 "wrapper", rather than a specific Java version
dependencies = [('Java', '1.8', '', True)]
dependencies = [('Java', '1.8', '', SYSTEM)]

builddependencies = [('JUnit', '4.12', versionsuffix)]

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Expand Up @@ -24,7 +24,7 @@ dependencies = [
('SAMtools', '1.10'),
('pigz', '2.4'),
('git', '2.23.0', '-nodocs'),
('git-lfs', '2.11.0', '', True),
('git-lfs', '2.11.0', '', SYSTEM),
]

# Download and install the reference database (1.8 GB)
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