Merge pull request #7048 from easybuilders/3.7.x

release EasyBuild v3.7.1

.travis.yml

@@ -43,8 +43,8 @@ install:
     - if [ ! -z $LMOD_VERSION ]; then source $(which install_eb_dep.sh) Lmod-${LMOD_VERSION} $HOME; fi
 before_script:
     - cd $TRAVIS_BUILD_DIR
-    # pull in develop so we can diff against it to obtain list of touched files
-    - if [ "x$TRAVIS_BRANCH" = 'xdevelop' ]; then git fetch -v origin ${TRAVIS_BRANCH}:${TRAVIS_BRANCH}; fi
+    # pull in target so we can diff against it to obtain list of touched files
+    - if [ "x$TRAVIS_BRANCH" != 'xmaster' ]; then git fetch -v origin ${TRAVIS_BRANCH}:${TRAVIS_BRANCH}; fi
 script:
     # make sure 'ml' alias is defined, otherwise sourcing the init script fails (silently) for Lmod (< 5.9.3)
     - if [ ! -z $MOD_INIT ] && [ ! -z $LMOD_VERSION ]; then alias ml=foobar; fi

RELEASE_NOTES

@@ -3,8 +3,52 @@ For more detailed information, please see the git log.
 
 These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html.
 
-The latest version of easybuild-easyconfig provides 9,628 easyconfig files, for 1,538 different software packages,
-30 different (compiler) toolchains, 13 software bundles and 1 meta-package.
+The latest version of easybuild-easyconfig provides 9,798 easyconfig files, for 1,564 different software packages,
+31 different (compiler) toolchains, 13 software bundles and 1 meta-package.
+
+v3.7.1 (October 18th 2018)
+--------------------------
+
+bugfix/update release
+- added easyconfigs for new toolchain foss/2018.08 with GCC/8.2.0 (#6992)
+- added example easyconfig files for 26 new software packages:
+  - ARCH (#6939), fbm (#6948), GenomeTester4 (#6970), GlobusConnectPersonal (#6974), MMseqs2 (#6964), NAG (#5772),
+    NAGfor (#5772), NSPR (#7005), NSS (#7005), NeuroKit (#6947), novoalign (#6944), OptiType (#6924),
+    OrthoFinder (#6964), pandas-datareader (#6938), pFUnit (#6949), PMIx (#6930), PSolver (#6888), PyDatastream (#6951),
+    PyFR (#6846), Pyomo (#6910), Quandl (#6950), RTG-Tools (#6862), seq2HLA (#6969), suds (#6951), UCX (#6931), XMLSec (#6929)
+- added additional easyconfigs for various supported software packages, including:
+  - binutils 2.31.1, dask 0.19.4, GCC(core) 8.2.0, OpenBLAS 0.3.3, OpenMPI 3.1.2, Pillow 5.3.0, PyCUDA 2018.1
+- minor enhancements, including:
+  - add clustree + plotly extensions (+ deps) for R 3.5.1 (#6901)
+  - add tclsh symlink to recent Tcl easyconfigs (#6915)
+  - update GROMACS 2016.3 with NVML patches (#6936)
+  - use make=make in build options for ParMGridGen easyconfigs (#6952)
+  - add Data::Dump as extension to Perl (dependency for GIMIC) (#7004)
+- various bug fixes, including:
+  - inhibit -Werror in binutils 2.26 as new system GCC has case fallthrough warnings (#5793)
+  - change fastStructure easyconfig to use custom easyblock (#6893)
+  - fix toolchain for tbb dependency in Bowtie2-2.3.4.2-foss-2018b.eb (#6927)
+  - fix uroot installation in R-3.5.1-foss-2018b (#6934)
+  - add missing Python packages in TensorFlow 1.10.x easyconfigs (#6940)
+  - add missing dep for Szip in 2017b builds of netCDF (#6942)
+  - fix missing comment from OpenBabel-2.4.1-fix-link-path-tests.patch (#6943)
+  - add patch to Python 3.6.1 - 3.6.3 that removes comment in comment (#6946)
+  - add missing ulimit_unlimited=True (see issue #6484) in the newest Python builds (#6959)
+  - solve 'version UUID_1.0 not found' problem in LibUUID easyconfigs (#6962)
+  - eliminate dependency on ancient problematic LibUUID library, replace with util-linux (#6963)
+  - force building of ccmake for CMake 3.12.1 + fix deps (#6967)
+  - fix broken installation for Python 3.6.2 & 3.6.3 with PyNaCl as dep for paramiko extension by explicitely including previous PyNaCl version as extension (#6971)
+  - fix source URL for ADMIXTURE (no https) + add SHA256 checksum (#6982)
+  - add missing NSS/DBus dependencies to Qt 5.10.1 easyconfigs built with foss toolchain to ensure that QtWebEngine component gets installed (#7005)
+  - add 'openssl' OS deps in Perl 5.28.0 easyconfig for Net::ssleay (#7008)
+  - add missing checksum for ipaddress extension in Python easyconfigs (#7021 and #7033)
+  - add missing extensions to Python 2.7.14 (#7022 and #7023), 3.6.2 (#7025), 3.6.3 (#7027) and 3.6.4 (#7029 and #7030)
+  - add missing OS dependencies for git (#7028)
+  - create default configuration for RTG-Tools (#7032)
+  - also run checks on changed files when target branch for PR is something different than 'develop' (#7034)
+- other changes:
+  - removed dead 'bzip.org' source URL for bzip2 source tarball (#6983)
+
 
 v3.7.0 (September 25th 2018)
 ----------------------------

easybuild/easyconfigs/a/ADMIXTURE/ADMIXTURE-1.3.0.eb

@@ -10,8 +10,9 @@ more rapidly using a fast numerical optimization algorithm."""
 
 toolchain = {'name': 'dummy', 'version': 'dummy'}
 
-source_urls = ['https://www.genetics.ucla.edu/software/%(namelower)s/binaries/']
+source_urls = ['http://www.genetics.ucla.edu/software/%(namelower)s/binaries/']
 sources = ['%(namelower)s_linux-%(version)s.tar.gz']
+checksums = ['41f209817a17981a717c9a4aa3d799da718ed080f3386e703927628c74ca6ca6']
 
 sanity_check_paths = {
     'files': ['admixture', 'admixture32'],

easybuild/easyconfigs/a/APR-util/APR-util-1.6.1-iomkl-2018a.eb

@@ -0,0 +1,30 @@
+easyblock = 'ConfigureMake'
+
+name = 'APR-util'
+version = '1.6.1'
+
+homepage = 'http://apr.apache.org/'
+description = "Apache Portable Runtime (APR) util libraries."
+
+toolchain = {'name': 'iomkl', 'version': '2018a'}
+
+source_urls = ['http://archive.apache.org/dist/apr/']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['b65e40713da57d004123b6319828be7f1273fbc6490e145874ee1177e112c459']
+
+dependencies = [
+    ('APR', '1.6.3'),
+    ('SQLite', '3.21.0'),
+    ('expat', '2.2.5'),
+]
+
+configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-sqlite3=$EBROOTSQLITE --with-expat=$EBROOTEXPAT "
+
+sanity_check_paths = {
+    'files': ["bin/apu-1-config", "lib/libaprutil-1.%s" % SHLIB_EXT, "lib/libaprutil-1.a"],
+    'dirs': ["include/apr-1"],
+}
+
+parallel = 1
+
+moduleclass = 'tools'

easybuild/easyconfigs/a/APR/APR-1.6.3-iomkl-2018a.eb

@@ -0,0 +1,20 @@
+easyblock = 'ConfigureMake'
+
+name = 'APR'
+version = '1.6.3'
+
+homepage = 'http://apr.apache.org/'
+description = "Apache Portable Runtime (APR) libraries."
+
+toolchain = {'name': 'iomkl', 'version': '2018a'}
+
+source_urls = ['http://archive.apache.org/dist/apr/']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['8fdabcc0004216c3588b7dca0f23d104dfe012a47e2bb6f13827534a6ee73aa7']
+
+sanity_check_paths = {
+    'files': ["bin/apr-1-config", "lib/libapr-1.%s" % SHLIB_EXT, "lib/libapr-1.a"],
+    'dirs': ["include/apr-1"],
+}
+
+moduleclass = 'tools'

easybuild/easyconfigs/a/ARCH/ARCH-4.5.0-intel-2018a-Python-3.6.4.eb

@@ -0,0 +1,48 @@
+easyblock = 'Bundle'
+
+name = 'ARCH'
+version = '4.5.0'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = "https://pypi.org/project/arch"
+description = """Autoregressive Conditional Heteroskedasticity (ARCH) and other tools for financial econometrics,
+ written in Python (with Cython and/or Numba used to improve performance)."""
+
+toolchain = {'name': 'intel', 'version': '2018a'}
+
+dependencies = [
+    ('Python', '3.6.4'),
+    ('numba', '0.37.0', versionsuffix),
+]
+
+exts_defaultclass = 'PythonPackage'
+exts_default_options = {
+    'download_dep_fail': True,
+    'use_pip': True,
+}
+
+
+exts_list = [
+    ('statsmodels', '0.9.0', {
+        'source_urls': ['https://pypi.python.org/packages/source/s/statsmodels'],
+        'checksums': ['6461f93a842c649922c2c9a9bc9d9c4834110b89de8c4af196a791ab8f42ba3b'],
+    }),
+    (name, version, {
+        'source_urls': ['https://pypi.python.org/packages/source/a/arch'],
+        'source_tmpl': 'arch-%(version)s.tar.gz',
+        'checksums': ['022a01cea492ffde934e23ed6d2bc7f9723df57c406f5739f41c672a91c8dea1'],
+        'installopts': "--install-option '--no-binary'",
+    }),
+]
+
+# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module
+full_sanity_check = True
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']}
+
+moduleclass = 'lib'

easybuild/easyconfigs/a/ASAP3/ASAP3-3.10.10-foss-2018b-Python-3.6.6.eb

@@ -0,0 +1,28 @@
+easyblock = "PythonPackage"
+
+name = 'ASAP3'
+version = '3.10.10'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'https://wiki.fysik.dtu.dk/asap/'
+description = """ASAP is a calculator for doing large-scale classical molecular
+dynamics within the Campos Atomic Simulation Environment (ASE)."""
+
+toolchain = {'name': 'foss', 'version': '2018b'}
+
+source_urls = [PYPI_LOWER_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['58cc70379ff3de727ad2e19882082c40a4780c72ae86e21decd15a8df1e202f0']
+
+dependencies = [
+    ('Python', '3.6.6'),
+    ('ASE', '3.16.2', versionsuffix),
+    ('OpenKIM-API', '1.9.7'),
+]
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s']
+}
+
+moduleclass = 'phys'

easybuild/easyconfigs/a/ASAP3/ASAP3-3.10.10-intel-2018b-Python-3.6.6.eb

@@ -0,0 +1,28 @@
+easyblock = "PythonPackage"
+
+name = 'ASAP3'
+version = '3.10.10'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'https://wiki.fysik.dtu.dk/asap/'
+description = """ASAP is a calculator for doing large-scale classical molecular
+dynamics within the Campos Atomic Simulation Environment (ASE)."""
+
+toolchain = {'name': 'intel', 'version': '2018b'}
+
+source_urls = [PYPI_LOWER_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['58cc70379ff3de727ad2e19882082c40a4780c72ae86e21decd15a8df1e202f0']
+
+dependencies = [
+    ('Python', '3.6.6'),
+    ('ASE', '3.16.2', versionsuffix),
+    ('OpenKIM-API', '1.9.7'),
+]
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s']
+}
+
+moduleclass = 'phys'

easybuild/easyconfigs/a/ASAP3/ASAP3-3.10.10-iomkl-2018b-Python-3.6.6.eb

@@ -0,0 +1,28 @@
+easyblock = "PythonPackage"
+
+name = 'ASAP3'
+version = '3.10.10'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'https://wiki.fysik.dtu.dk/asap/'
+description = """ASAP is a calculator for doing large-scale classical molecular
+dynamics within the Campos Atomic Simulation Environment (ASE)."""
+
+toolchain = {'name': 'iomkl', 'version': '2018b'}
+
+source_urls = [PYPI_LOWER_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['58cc70379ff3de727ad2e19882082c40a4780c72ae86e21decd15a8df1e202f0']
+
+dependencies = [
+    ('Python', '3.6.6'),
+    ('ASE', '3.16.2', versionsuffix),
+    ('OpenKIM-API', '1.9.7'),
+]
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s']
+}
+
+moduleclass = 'phys'

easybuild/easyconfigs/a/ASE/ASE-3.16.2-foss-2018b-Python-3.6.6.eb

@@ -0,0 +1,31 @@
+easyblock = 'PythonPackage'
+
+name = 'ASE'
+version = '3.16.2'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'https://wiki.fysik.dtu.dk/ase'
+description = """ASE is a python package providing an open source Atomic Simulation Environment
+ in the Python scripting language."""
+
+toolchain = {'name': 'foss', 'version': '2018b'}
+
+source_urls = [PYPI_LOWER_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['5e63e7dc18fd13dcc3cb46ab3de019375b9d62c6c3a845a99f34b6928251f4c2']
+
+dependencies = [
+    ('Python', '3.6.6'),
+    ('Tkinter', '%(pyver)s', '-Python-%(pyver)s'),
+    ('matplotlib', '3.0.0', '-Python-%(pyver)s'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/ase'],
+    'dirs': [],
+}
+
+# make sure Tkinter is available, otherwise 'ase gui' will not work
+sanity_check_commands = ["python -c 'import tkinter' "]
+
+moduleclass = 'chem'

easybuild/easyconfigs/a/ASE/ASE-3.16.2-intel-2018b-Python-3.6.6.eb

@@ -0,0 +1,31 @@
+easyblock = 'PythonPackage'
+
+name = 'ASE'
+version = '3.16.2'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'https://wiki.fysik.dtu.dk/ase/'
+description = """ASE is a python package providing an open source Atomic Simulation Environment
+ in the Python scripting language."""
+
+toolchain = {'name': 'intel', 'version': '2018b'}
+
+source_urls = [PYPI_LOWER_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['5e63e7dc18fd13dcc3cb46ab3de019375b9d62c6c3a845a99f34b6928251f4c2']
+
+dependencies = [
+    ('Python', '3.6.6'),
+    ('Tkinter', '%(pyver)s', '-Python-%(pyver)s'),
+    ('matplotlib', '3.0.0', '-Python-%(pyver)s'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/ase'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+# make sure Tkinter is available, otherwise 'ase gui' will not work
+sanity_check_commands = ["python -c 'import tkinter' "]
+
+moduleclass = 'chem'

easybuild/easyconfigs/a/ASE/ASE-3.16.2-iomkl-2018b-Python-3.6.6.eb

@@ -0,0 +1,31 @@
+easyblock = 'PythonPackage'
+
+name = 'ASE'
+version = '3.16.2'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'https://wiki.fysik.dtu.dk/ase/'
+description = """ASE is a python package providing an open source Atomic Simulation Environment
+ in the Python scripting language."""
+
+toolchain = {'name': 'iomkl', 'version': '2018b'}
+
+source_urls = [PYPI_LOWER_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['5e63e7dc18fd13dcc3cb46ab3de019375b9d62c6c3a845a99f34b6928251f4c2']
+
+dependencies = [
+    ('Python', '3.6.6'),
+    ('Tkinter', '%(pyver)s', '-Python-%(pyver)s'),
+    ('matplotlib', '3.0.0', '-Python-%(pyver)s'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/ase'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+# make sure Tkinter is available, otherwise 'ase gui' will not work
+sanity_check_commands = ["python -c 'import tkinter' "]
+
+moduleclass = 'chem'

easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.2.2-foss-2018b.eb

@@ -0,0 +1,34 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+
+easyblock = 'MakeCp'
+
+name = 'AdapterRemoval'
+version = '2.2.2'
+
+homepage = 'https://github.com/MikkelSchubert/%(namelower)s'
+description = """AdapterRemoval searches for and removes remnant adapter sequences
+ from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases
+ from the 3' end of reads following adapter removal."""
+
+toolchain = {'name': 'foss', 'version': '2018b'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/MikkelSchubert/%(namelower)s/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['99832546428a1e9463a565fa726844a0559828bda9428b2b51ef6b3558079b67']
+
+files_to_copy = [(['build/%(name)s'], 'bin'), (['build/%(name)s.1'], 'share/man/man1')]
+
+dependencies = [
+    ('bzip2', '1.0.6'),
+    ('zlib', '1.2.11'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/%(name)s'],
+    'dirs': ['share']
+}
+
+sanity_check_commands = [('AdapterRemoval', '--version')]
+
+moduleclass = 'bio'