{bio}[foss/2020b] PPanGGOLiN v1.1.136 + dependencies

easybuild/easyconfigs/a/ARAGORN/ARAGORN-1.2.41-foss-2020b.eb

@@ -0,0 +1,43 @@
+# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/
+# Author: Pablo Escobar Lopez
+# sciCORE - University of Basel
+# SIB Swiss Institute of Bioinformatics
+# Updated: Denis Kristak
+
+easyblock = 'CmdCp'
+
+name = 'ARAGORN'
+version = '1.2.41'
+
+homepage = 'http://mbio-serv2.mbioekol.lu.se/ARAGORN/'
+description = "http://www.ansikte.se/ARAGORN/"
+
+toolchain = {'name': 'foss', 'version': '2020b'}
+
+source_urls = ['http://www.ansikte.se/ARAGORN/Downloads/']
+sources = [
+    {'filename': '%(namelower)s%(version)s.c', 'extract_cmd': 'cp %s aragorn.c'},
+    {'filename': 'aragorn.1', 'extract_cmd': 'cp %s aragorn.1'}  # man page
+]
+checksums = [
+    '92a31cc5c0b0ad16d4d7b01991989b775f07d2815df135fe6e3eab88f5e97f4a',  # aragorn1.2.41.c
+    '6e30f6d9da644197064744f033176969e77855964ed8d50ea00c38a3aea2c92e',  # aragorn.1
+]
+
+cmds_map = [
+    (".*", "$CC $CFLAGS -o aragorn aragorn.c"),  # TODO since there are 2 sources, install command repeats twice
+]
+
+files_to_copy = [
+    (['aragorn'], 'bin'),
+    (['aragorn.1'], 'share/man/man1'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/aragorn'],
+    'dirs': ['share/man'],
+}
+
+sanity_check_commands = ['aragorn --help']
+
+moduleclass = 'bio'

easybuild/easyconfigs/g/genoPlotR/genoPlotR-0.8.11-foss-2020b.eb

@@ -0,0 +1,28 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Author: Denis Kristak
+easyblock = 'RPackage'
+
+name = 'genoPlotR'
+version = '0.8.11'
+
+homepage = 'https://cran.r-project.org/web/packages/genoPlotR/index.html'
+description = """Draws gene or genome maps and comparisons between these, in a publication-grade manner.
+Starting from simple, common files, it will draw postscript or PDF files that can be sent as such to journals.
+"""
+
+toolchain = {'name': 'foss', 'version': '2020b'}
+
+source_urls = ['https://cran.r-project.org/src/contrib/']
+sources = ['%s_%s.tar.gz' % (name, version)]
+checksums = ['f127f7fe8b19c899ecfdf98bf69d2e18926afb593a72fc40097acca66d401607']
+
+dependencies = [
+    ('R', '4.0.3'),
+]
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['genoPlotR'],
+}
+
+moduleclass = 'vis'

easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-foss-2020b.eb

@@ -0,0 +1,36 @@
+##
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+#
+# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA
+# Authors::   Cedric Laczny <cedric.laczny@uni.lu>, Fotis Georgatos <fotis@cern.ch>
+# License::   MIT/GPL
+# Updated:: Denis Kristak (INUITS)
+# $Id$
+#
+# This work implements a part of the HPCBIOS project and is a component of the policy:
+# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html
+##
+
+easyblock = 'ConfigureMake'
+
+name = 'Infernal'
+version = "1.1.4"
+
+homepage = 'http://eddylab.org/infernal/'
+description = """Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases
+ for RNA structure and sequence similarities."""
+
+toolchain = {'name': 'foss', 'version': '2020b'}
+toolchainopts = {'optarch': True, 'pic': True}
+
+source_urls = ['http://eddylab.org/%(namelower)s']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['f9493c7dee9fbf25f6405706818883d24b9f5e455121a0662c96c8f0307f95fc']
+
+sanity_check_paths = {
+    'files': ['bin/cm%s' % x for x in ['align', 'build', 'calibrate', 'convert', 'emit',
+                                       'fetch', 'press', 'scan', 'search', 'stat']],
+    'dirs': []
+}
+
+moduleclass = 'bio'

easybuild/easyconfigs/p/PPanGGOLiN/PPanGGOLiN-1.1.136-foss-2020b.eb

@@ -0,0 +1,74 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Author: Denis Kristak
+easyblock = 'PythonPackage'
+
+name = 'PPanGGOLiN'
+version = '1.1.136'
+
+homepage = 'https://github.com/labgem/PPanGGOLiN'
+description = """
+PPanGGOLiN is a software suite used to create and manipulate prokaryotic
+pangenomes from a set of either genomic DNA sequences or provided genome annotations. It is designed
+to scale up to tens of thousands of genomes. It has the specificity to partition the pangenome using
+a statistical approach rather than using fixed thresholds which gives it the ability to work with low-quality
+data such as Metagenomic Assembled Genomes (MAGs) or Single-cell Amplified Genomes (SAGs) thus taking advantage
+of large scale environmental studies and letting users study the pangenome of uncultivable species.
+"""
+
+toolchain = {'name': 'foss', 'version': '2020b'}
+
+source_urls = ['https://github.com/labgem/%(name)s/archive/refs/tags/']
+sources = ['%(version)s.tar.gz']
+patches = ['PPanGGOLiN-1.1.136_new_compiler_compatibility.patch']
+checksums = [
+    '41f814f0b9331a8f0e04f09c698cef6200429990ce726339b5bb320bb7943a70',  # 1.1.136.tar.gz
+    # PPanGGOLiN-1.1.136_new_compiler_compatibility.patch
+    'ae4dadf2f7469e4c3d56b10236aa7812bfe6f5ed231676364f7c3f0d42e8facf',
+]
+
+dependencies = [
+    ('Python', '3.8.6'),
+    ('tqdm', '4.56.2'),
+    ('PyTables', '3.6.1'),
+    ('prodigal', '2.6.3'),
+    ('ARAGORN', '1.2.41'),
+    ('Infernal', '1.1.4'),
+    ('MMseqs2', '13-45111'),
+    ('networkx', '2.5'),
+    ('SciPy-bundle', '2020.11'),
+    ('plotly.py', '4.14.3'),
+    ('gmpy2', '2.1.0b5'),
+    ('genoPlotR', '0.8.11'),
+    ('MAFFT', '7.475', '-with-extensions'),
+    ('rpy2', '3.4.5'),
+]
+
+configopts = '-DBLAS_LIBRARIES=$EBROOTOPENBLAS/lib/libopenblas.%s ' % SHLIB_EXT
+configopts += '-DLAPACK_LIBRARIES=$EBROOTOPENBLAS/lib/libopenblas.%s ' % SHLIB_EXT
+
+use_pip = True
+sanity_pip_check = True
+download_dep_fail = True
+
+exts_default_options = {
+    'source_urls': [PYPI_SOURCE],
+    'use_pip': True,
+    'download_dep_fail': True,
+
+}
+exts_defaultclass = 'PythonPackage'
+
+exts_list = [
+    ('colorlover', '0.3.0', {
+        'checksums': ['b8fb7246ab46e1f5e6715649453c1762e245a515de5ff2d2b4aab7a6e67fa4e2'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/ppanggolin'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ['ppanggolin --help']
+
+moduleclass = 'bio'

easybuild/easyconfigs/p/PPanGGOLiN/PPanGGOLiN-1.1.136_new_compiler_compatibility.patch

@@ -0,0 +1,15 @@
+adding -fcommon flag since it was removed from defaults in newer compilers
+author: Denis Kristak (INUITS)
+diff -ruN PPanGGOLiN-1.1.136_orig/setup.py PPanGGOLiN-1.1.136/setup.py
+--- PPanGGOLiN-1.1.136_orig/setup.py	2021-11-23 10:32:07.957348000 +0100
++++ PPanGGOLiN-1.1.136/setup.py	2021-11-23 10:43:58.316011000 +0100
+@@ -28,7 +28,8 @@
+                 "Programming Language :: Python :: 3",
+                 "Topic :: Scientific/Engineering :: Bio-Informatics"],
+         entry_points={"console_scripts":["ppanggolin = ppanggolin.main:main"]},
+-        ext_modules = [Extension(name = "nem_stats",sources =[NEM_DIR_PATH+'nem_stats.pyx',
++        extra_compile_args=['-fcommon'],
++        ext_modules = [Extension(name = "nem_stats", extra_compile_args=['-fcommon'], sources =[NEM_DIR_PATH+'nem_stats.pyx',
+                                                                         NEM_DIR_PATH+'nem_exe.c',
+                                                                         NEM_DIR_PATH+'nem_alg.c',
+                                                                         NEM_DIR_PATH+'nem_nei.c',

easybuild/easyconfigs/r/rpy2/rpy2-3.4.5-foss-2020b.eb

@@ -0,0 +1,60 @@
+# Author: Pavel Grochal (INUITS)
+# Updated: Denis Kristak (INUITS)
+# License: GPLv2
+
+easyblock = 'PythonBundle'
+
+name = 'rpy2'
+version = '3.4.5'
+
+homepage = 'https://rpy2.bitbucket.io/'
+description = """rpy2 is an interface to R running embedded in a Python process."""
+
+toolchain = {'name': 'foss', 'version': '2020b'}
+
+dependencies = [
+    ('Python', '3.8.6'),
+    ('R', '4.0.3'),
+    ('IPython', '7.18.1'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('simplegeneric', '0.8.1', {
+        'source_tmpl': '%(name)s-%(version)s.zip',
+        'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'],
+    }),
+    ('tzlocal', '4.1', {
+        'checksums': ['0f28015ac68a5c067210400a9197fc5d36ba9bc3f8eaf1da3cbd59acdfed9e09'],
+    }),
+    ('cffi', '1.15.0', {
+        'checksums': ['920f0d66a896c2d99f0adbb391f990a84091179542c205fa53ce5787aff87954'],
+    }),
+    ('tzdata', '2021.5', {
+        'checksums': ['68dbe41afd01b867894bbdfd54fa03f468cfa4f0086bfb4adcd8de8f24f3ee21'],
+    }),
+    ('backports-zoneinfo', '0.2.1', {
+        'modulename': 'backports.zoneinfo',
+        'source_tmpl': 'backports.zoneinfo-%(version)s.tar.gz',
+        'checksums': ['fadbfe37f74051d024037f223b8e001611eac868b5c5b06144ef4d8b799862f2'],
+    }),
+    ('pytz-deprecation-shim', '0.1.0.post0', {
+        'source_tmpl': 'pytz_deprecation_shim-%(version)s.tar.gz',
+        'checksums': ['af097bae1b616dde5c5744441e2ddc69e74dfdcb0c263129610d85b87445a59d'],
+    }),
+    (name, version, {
+        'checksums': ['5d31a5ea43f5a59f6dec30faca87edb01fc9b8affa0beae96a99be923bd7dab3'],
+    }),
+]
+
+# sanity_check_commands = [
+#     "pytest --pyargs rpy2 "
+#     # Disable tests which requires X11 present othewise it crashes with
+#     # "unable to open connection to X11 display" error
+#     "--ignore=lib/python3.8/site-packages/rpy2/tests/ipython/test_rmagic.py "
+#     "--ignore=lib/python3.8/site-packages/rpy2/tests/robjects/lib/test_grdevices.py "
+# ]
+
+moduleclass = 'tools'