From ac5aab030a9693f0c411fbfa3f4ea72fcd4ade96 Mon Sep 17 00:00:00 2001
From: Sebastian Achilles <s.achilles@fz-juelich.de>
Date: Mon, 24 Jan 2022 15:00:54 +0100
Subject: [PATCH] adding easyconfigs:
Biopython-1.79-gcccoremkl-11.2.0-2021.4.0.eb,
networkx-2.6.3-gcccoremkl-11.2.0-2021.4.0.eb,
MDAnalysis-2.0.0-gcccoremkl-11.2.0-2021.4.0.eb
---
...opython-1.79-gcccoremkl-11.2.0-2021.4.0.eb | 42 +++++++++++++++++
...alysis-2.0.0-gcccoremkl-11.2.0-2021.4.0.eb | 46 +++++++++++++++++++
...tworkx-2.6.3-gcccoremkl-11.2.0-2021.4.0.eb | 24 ++++++++++
3 files changed, 112 insertions(+)
create mode 100644 Golden_Repo/b/Biopython/Biopython-1.79-gcccoremkl-11.2.0-2021.4.0.eb
create mode 100644 Golden_Repo/m/MDAnalysis/MDAnalysis-2.0.0-gcccoremkl-11.2.0-2021.4.0.eb
create mode 100644 Golden_Repo/n/networkx/networkx-2.6.3-gcccoremkl-11.2.0-2021.4.0.eb
diff --git a/Golden_Repo/b/Biopython/Biopython-1.79-gcccoremkl-11.2.0-2021.4.0.eb b/Golden_Repo/b/Biopython/Biopython-1.79-gcccoremkl-11.2.0-2021.4.0.eb
new file mode 100644
index 000000000..c42b6f2eb
--- /dev/null
+++ b/Golden_Repo/b/Biopython/Biopython-1.79-gcccoremkl-11.2.0-2021.4.0.eb
@@ -0,0 +1,42 @@
+easyblock = 'PythonPackage'
+
+name = 'Biopython'
+version = '1.79'
+
+homepage = 'https://www.biopython.org'
+description = """Biopython is a set of freely available tools for biological
+ 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': 'gcccoremkl', 'version': '11.2.0-2021.4.0'}
+
+source_urls = ['https://biopython.org/DIST']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['edb07eac99d3b8abd7ba56ff4bedec9263f76dfc3c3f450e7d2e2bcdecf8559b']
+
+dependencies = [
+ ('Python', '3.9.6'),
+ ('SciPy-bundle', '2021.10'),
+]
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+# Run only tests that don't require internet connection
+runtest = 'python setup.py test --offline'
+
+sanity_check_paths = {
+ 'files': [],
+ 'dirs': ['lib/python%(pyshortver)s/site-packages/Bio',
+ 'lib/python%(pyshortver)s/site-packages/BioSQL']
+}
+
+# extra check to ensure numpy dependency is available
+sanity_check_commands = ["python -c 'import Bio.MarkovModel'"]
+
+options = {'modulename': 'Bio'}
+
+moduleclass = 'bio'
diff --git a/Golden_Repo/m/MDAnalysis/MDAnalysis-2.0.0-gcccoremkl-11.2.0-2021.4.0.eb b/Golden_Repo/m/MDAnalysis/MDAnalysis-2.0.0-gcccoremkl-11.2.0-2021.4.0.eb
new file mode 100644
index 000000000..10262dd9b
--- /dev/null
+++ b/Golden_Repo/m/MDAnalysis/MDAnalysis-2.0.0-gcccoremkl-11.2.0-2021.4.0.eb
@@ -0,0 +1,46 @@
+easyblock = 'PythonBundle'
+
+name = 'MDAnalysis'
+version = '2.0.0'
+
+homepage = 'https://www.mdanalysis.org/'
+description = """MDAnalysis is an object-oriented Python library to analyze trajectories from molecular dynamics (MD)
+simulations in many popular formats."""
+
+toolchain = {'name': 'gcccoremkl', 'version': '11.2.0-2021.4.0'}
+
+dependencies = [
+ ('Python', '3.9.6'),
+ ('SciPy-bundle', '2021.10'),
+ ('matplotlib', '3.4.3'),
+ ('Biopython', '1.79'),
+ ('networkx', '2.6.3'),
+ ('tqdm', '4.62.3'),
+]
+
+use_pip = True
+download_dep_fail = True
+sanity_pip_check = True
+
+exts_list = [
+ ('GridDataFormats', '0.6.0', {
+ 'modulename': 'gridData',
+ 'checksums': ['f14e00e8b795f8021f6069935e1133352224775c9bd97f395beb2bcd64a19b86'],
+ }),
+ ('gsd', '2.5.1', {
+ 'checksums': ['76bf228b1d8e95e7d6a334e8cc7712c0bd8c256148007f7ce88a489c21996593'],
+ }),
+ ('msgpack', '1.0.3', {
+ 'checksums': ['51fdc7fb93615286428ee7758cecc2f374d5ff363bdd884c7ea622a7a327a81e'],
+ }),
+ ('mmtf-python', '1.1.2', {
+ 'modulename': 'mmtf',
+ 'checksums': ['a5caa7fcd2c1eaa16638b5b1da2d3276cbd3ed3513f0c2322957912003b6a8df'],
+ }),
+ (name, version, {
+ 'modulename': name,
+ 'checksums': ['aa3079d1a82305eba58cf567fac8fc231940184ed88f9a4451be8433f4a06d3e'],
+ }),
+]
+
+moduleclass = 'bio'
diff --git a/Golden_Repo/n/networkx/networkx-2.6.3-gcccoremkl-11.2.0-2021.4.0.eb b/Golden_Repo/n/networkx/networkx-2.6.3-gcccoremkl-11.2.0-2021.4.0.eb
new file mode 100644
index 000000000..5f378c9c6
--- /dev/null
+++ b/Golden_Repo/n/networkx/networkx-2.6.3-gcccoremkl-11.2.0-2021.4.0.eb
@@ -0,0 +1,24 @@
+easyblock = 'PythonPackage'
+
+name = 'networkx'
+version = '2.6.3'
+
+homepage = 'https://pypi.python.org/pypi/networkx'
+description = """NetworkX is a Python package for the creation, manipulation,
+and study of the structure, dynamics, and functions of complex networks."""
+
+toolchain = {'name': 'gcccoremkl', 'version': '11.2.0-2021.4.0'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['c0946ed31d71f1b732b5aaa6da5a0388a345019af232ce2f49c766e2d6795c51']
+
+dependencies = [
+ ('Python', '3.9.6'),
+ ('SciPy-bundle', '2021.10'), # required for numpy, scipy, ...
+]
+
+use_pip = True
+download_dep_fail = True
+sanity_pip_check = True
+
+moduleclass = 'tools'
--
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