{bio}[foss/2020b] LncLOOM v2.0, MAFFT v7.475

easybuild/easyconfigs/g/Gurobi/Gurobi-9.1.1-GCCcore-10.2.0.eb

@@ -0,0 +1,26 @@
+name = 'Gurobi'
+version = '9.1.1'
+
+homepage = 'https://www.gurobi.com'
+description = """The Gurobi Optimizer is a state-of-the-art solver for mathematical programming.
+The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern 
+architectures and multi-core processors, using the most advanced implementations of the 
+latest algorithms."""
+
+toolchain = {'name': 'GCCcore', 'version': '10.2.0'}
+
+source_urls = ['https://packages.gurobi.com/%(version_major_minor)s/']
+sources = ['%(namelower)s%(version)s_linux64.tar.gz']
+checksums = ['ba57a83656bf6ab481e1114f5596664385a88a35a47ae51aa2ac307f58aaa44a']
+
+builddependencies = [
+    ('binutils', '2.35'),
+]
+
+dependencies = [
+    ('Python', '3.8.6'),
+]
+
+license_file = HOME + '/licenses/%(name)s/%(namelower)s.lic'
+
+moduleclass = 'math'

easybuild/easyconfigs/l/LncLOOM/LncLOOM-2.0-config-from-environment.patch

@@ -0,0 +1,77 @@
+Specify for_eclip_annotation.txt/for_track_annotation.txt via the environment
+variables LNCLOOM_ECLIP_CONFIG/LNCLOOM_TRACK_CONFIG instead of hardcoded paths.
+
+Relax biopython dependency (<= 1.78).
+
+Author: Jakub Zárybnický <jakub@zarybnicky.com>
+
+diff -ru LncLOOMv2/LncLOOMv2/LncLOOM.py LncLOOMv2-edit/LncLOOMv2/LncLOOM.py
+--- LncLOOMv2/LncLOOMv2/LncLOOM.py	2021-02-18 10:45:46.000000000 +0100
++++ LncLOOMv2-edit/LncLOOMv2/LncLOOM.py	2021-03-01 14:06:44.600554538 +0100
+@@ -115,14 +115,24 @@
+
+
+     if args.eclip== True:
+-        efile = os.path.join(os.path.dirname(__file__), 'src', 'for_eclip_annotation.txt')
++        try:
++            efile = os.environ['LNCLOOM_ECLIP_CONFIG']
++        except KeyError:
++            print('To use --eclip, specify a config file via the '
++                  'LNCLOOM_ECLIP_CONFIG environment variable')
++            exit()
+         if not os.path.exists(str(efile)):
+             print("ERROR! Cannot find src file:"+str(efile))
+             Valid = False
+
+     if args.track == True:
+         #check bedfile_output.txt is found
+-        tfile = os.path.join(os.path.dirname(__file__), 'src', 'for_track_output.txt')
++        try:
++            tfile = os.environ['LNCLOOM_TRACK_CONFIG']
++        except KeyError:
++            print('To use --track, specify a config file via the '
++                  'LNCLOOM_TRACK_CONFIG environment variable')
++            exit()
+         if not os.path.exists(tfile):
+             print("ERROR! Cannot find src file:for_track_output.txt")
+             Valid = False
+@@ -276,7 +286,12 @@
+         track_bed = ''
+         format_file = True
+         if track ==True:
+-            tfile = os.path.join(os.path.dirname(__file__), 'src', 'for_track_output.txt')
++            try:
++                tfile = os.environ['LNCLOOM_TRACK_CONFIG']
++            except KeyError:
++                print('To use --track, specify a config file via the '
++                      'LNCLOOM_TRACK_CONFIG environment variable')
++                exit()
+             b = open(tfile,'r')
+             blines = b.readlines()
+             b.close()
+@@ -420,7 +435,12 @@
+         #Annotate eCLIP: here we are annotating and creating tables for all combined and sub-kmers in the selected query layer.
+         #This only needs to be done once, as the annotations for all k-mers will be stored - loop not needed here
+         if eCLIP==True:
+-            efile = os.path.join(os.path.dirname(__file__), 'src', 'for_eclip_annotation.txt')
++            try:
++                efile = os.environ['LNCLOOM_ECLIP_CONFIG']
++            except KeyError:
++                print('To use --eclip, specify a config file via the '
++                      'LNCLOOM_ECLIP_CONFIG environment variable')
++                exit()
+             e = open(efile,'r')
+             elines = e.readlines()
+             e.close()
+diff -ru LncLOOMv2/setup.py LncLOOMv2-edit/setup.py
+--- LncLOOMv2/setup.py	2021-02-18 10:45:46.000000000 +0100
++++ LncLOOMv2-edit/setup.py	2021-03-01 14:01:42.430780746 +0100
+@@ -10,7 +10,7 @@
+     packages=find_packages(include=['LncLOOMv2', 'LncLOOMv2.*']),
+     install_requires=[
+         'networkx',
+-        'numpy>=1.14.5','biopython<=1.76','pulp','pyBigWig'
++        'numpy>=1.14.5','biopython<=1.78','pulp','pyBigWig'
+     ],
+
+     entry_points={

easybuild/easyconfigs/l/LncLOOM/LncLOOM-2.0-foss-2020b.eb

@@ -0,0 +1,71 @@
+easyblock = 'PythonBundle'
+
+name = 'LncLOOM'
+version = '2.0'
+
+homepage = 'https://github.com/lncLOOM/lncLOOMv2/'
+description = """LncLOOM is a graph-based framework that uses integer
+programming to identify combinations of short motifs that are deeply conserved
+in rapidly evolving sequences."""
+
+toolchain = {'name': 'foss', 'version': '2020b'}
+
+dependencies = [
+    ('Python', '3.8.6'),
+    ('SciPy-bundle', '2020.11'),
+    ('MAFFT', '7.475', '-with-extensions'),
+    ('BLAST+', '2.11.0'),
+    ('Gurobi', '9.1.1'),
+    ('Biopython', '1.78'),
+]
+
+use_pip = True
+
+exts_default_options = {'source_urls': [PYPI_SOURCE]}
+exts_list = [
+    ('amply', '0.1.4', {
+        'checksums': ['cb12dcb49d16b168c02be128a1527ecde50211e4bd94af76ff4e67707f5a2d38'],
+    }),
+    ('networkx', '2.5', {
+        'checksums': ['7978955423fbc9639c10498878be59caf99b44dc304c2286162fd24b458c1602'],
+    }),
+    ('PuLP', '2.4', {
+        'source_tmpl': '%(version)s.tar.gz',
+        'source_urls': ['https://github.com/coin-or/pulp/archive/'],
+        'checksums': ['d52d52b6078ea2c503b33814738866902d661cfe60d7a76251d50423e4af3ad0'],
+    }),
+    ('pyBigWig', '0.3.18', {
+        'modulename': 'pyBigWig',
+        'checksums': ['4c2a8c571b4100ad7c4c318c142eb48558646be52aaab28215a70426f5be31bc'],
+    }),
+    (name, version, {
+        'modulename': 'LncLOOMv2',
+        'patches': ['LncLOOM-2.0-config-from-environment.patch'],
+        'source_tmpl': '75b82aeb359b65998770577e7516ed54845ba66c.tar.gz',
+        'source_urls': ['https://github.com/lncLOOM/LncLOOMv2/archive/'],
+        'checksums': [
+            # 75b82aeb359b65998770577e7516ed54845ba66c.tar.gz
+            'cc00beec1ddfc879c94948d9e7b7736b2b5156617b8724927d7459e6b88d0e59',
+            # LncLOOM-2.0-config-from-environment.patch
+            'bd8f13af556efe062e70ca06805fb0d1a6046bd50a59eaf69fb0014a844f169d',
+        ],
+    }),
+]
+
+postinstallcmds = [
+    'chmod +x %(installdir)s/lib/python%(pyshortver)s/site-packages/LncLOOMv2/src/blat',
+    'find %(installdir)s/lib/python%(pyshortver)s/site-packages/pulp/'
+    ' -executable -type f -exec chmod +x {} \\;',
+]
+
+sanity_pip_check = True
+sanity_check_paths = {
+    'files': ['bin/LncLOOM'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/LncLOOMv2'],
+}
+sanity_check_commands = [
+    'pulptest',
+    'LncLOOM --help',
+]
+
+moduleclass = 'bio'

easybuild/easyconfigs/m/MAFFT/MAFFT-7.475-gompi-2020b-with-extensions.eb

@@ -0,0 +1,52 @@
+easyblock = 'Bundle'
+
+name = 'MAFFT'
+version = '7.475'
+versionsuffix = '-with-extensions'
+
+homepage = 'https://mafft.cbrc.jp/alignment/software/source.html'
+description = """MAFFT is a multiple sequence alignment program for unix-like operating systems.
+It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment
+of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc."""
+
+toolchain = {'name': 'gompi', 'version': '2020b'}
+toolchainopts = {'usempi': True}
+
+default_easyblock = 'ConfigureMake'
+default_component_specs = {
+    'source_urls': ['https://mafft.cbrc.jp/alignment/software/'],
+    'sources': ['mafft-%(version)s%(versionsuffix)s-src.tgz'],
+    'checksums': ['bb6973ae089ea18cfbd3861a5b9d2c8b7e1543a1fdc78ac2d7cd8dbe3443f319'],
+    'skipsteps': ['configure'],
+    'installopts': 'PREFIX=%(installdir)s',
+}
+
+components = [
+    (name, version, {
+        'start_dir': 'mafft-%(version)s%(versionsuffix)s/core',
+    }),
+    ('%s Extensions' % name, version, {
+        'start_dir': 'mafft-%(version)s%(versionsuffix)s/extensions',
+    }),
+    ('%s MPI' % name, version, {
+        'start_dir': 'mafft-%(version)s%(versionsuffix)s/MPI',
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/mafft'] + ['libexec/mafft/%s' % x for x in [
+        'mxscarnamod',  # installed by MAFFT Extensions
+        'mpiscript', 'nodepair_mpi',  # installed by MAFFT MPI
+    ]],
+    'dirs': ['libexec/mafft'],
+}
+
+sanity_check_commands = ['mafft --version']
+
+modextrapaths = {'MAFFT_BINARIES': 'libexec/mafft'}
+
+modextravars = {'MAFFT_N_THREADS_PER_PROCESS': '1'}
+# MAFFT MPI requires other environment variables that depend on job resources
+# More information at at https://mafft.cbrc.jp/alignment/software/mpi.html
+
+moduleclass = 'bio'