{bio,tools}[foss/2025b,gompi/2025b] ModPipe v2.3.1, HH-suite v3.3.0-2025-08-12

easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-2025-08-12-gompi-2025b.eb

@@ -0,0 +1,99 @@
+##
+# This file is an EasyBuild recipy as per https://github.com/easybuilders/easybuild
+#
+# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA
+# Authors::   Fotis Georgatos <[email protected]>
+# License::   MIT/GPL
+# $Id$
+#
+# This work implements a part of the HPCBIOS project and is a component of the policy:
+# https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html
+##
+# Contribution from the NIHR Biomedical Research Centre
+# Guy's and St Thomas' NHS Foundation Trust and King's College London
+# uploaded by J. Sassmannshausen
+
+easyblock = 'CMakeMake'
+
+name = 'HH-suite'
+version = '3.3.0-2025-08-12'
+local_commit = '43095e4'
+
+homepage = 'https://github.com/soedinglab/hh-suite'
+description = """The HH-suite is an open-source software package
+ for sensitive protein sequence searching based on the pairwise
+ alignment of hidden Markov models (HMMs)."""
+
+toolchain = {'name': 'gompi', 'version': '2025b'}
+
+source_urls = ['https://github.com/soedinglab/hh-suite/archive/']
+sources = [{
+    'download_filename': f'{local_commit}.tar.gz',
+    'filename': f'%(name)s-%(version)s-{local_commit}.tar.gz',
+}]
+checksums = ['d9145fe93d1e6d35ebad9604998356406fdfd91239d949b19a5e60bc641d04d0']
+
+builddependencies = [
+    ('CMake', '4.0.3'),
+]
+
+dependencies = [
+    ('Perl', '5.40.2'),
+    ('Python', '3.13.5'),
+]
+
+# fix cmake policy version - CMAKE v4 is not compatible with versions < v3.5
+configopts = '-DCMAKE_POLICY_VERSION_MINIMUM=3.5'
+
+# ModPipe is looking for scripts in lib/hh dir
+postinstallcmds = ["mkdir -p %(installdir)s/lib/hh && ln -s %(installdir)s/scripts %(installdir)s/lib/hh/scripts"]
+
+_binaries_help = [
+    'cstranslate', 'cstranslate_mpi', 'hhalign', 'hhalign_mpi', 'hhalign_omp', 'hhconsensus',
+    'hhfilter', 'hhmake'
+]
+
+_binaries_h = [
+    'a3m_database_extract', 'a3m_database_filter', 'a3m_database_reduce', 'a3m_extract', 'a3m_reduce',
+    'hhblits', 'hhblits_ca3m', 'hhblits_mpi', 'hhblits_omp', 'hhsearch', 'hhsearch_mpi', 'hhsearch_omp'
+]
+
+_binaries_version = ['ffindex_build', 'ffindex_from_fasta', 'ffindex_modify']
+
+_binaries_v = ['ffindex_from_fasta_with_split']
+
+_binaries_helpless = [
+    'ffindex_apply', 'ffindex_apply_mpi', 'ffindex_get',
+    'ffindex_order', 'ffindex_reduce', 'ffindex_unpack'
+]
+
+_scriptfiles = ['hhmakemodel.py', 'hh_reader.py', 'hhsuitedb.py', 'cif2fasta.py']
+
+fix_perl_shebang_for = ['scripts/*pl']
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in _binaries_help] +
+             ['bin/%s' % x for x in _binaries_h] +
+             ['bin/%s' % x for x in _binaries_version] +
+             ['bin/%s' % x for x in _binaries_v] +
+             ['bin/%s' % x for x in _binaries_helpless] +
+             ['scripts/%s' % y for y in _scriptfiles],
+    'dirs': ['data', 'scripts', 'lib/hh']
+}
+
+sanity_check_commands = ['%s --help' % x for x in _binaries_help]
+sanity_check_commands += ['%s -h' % x for x in _binaries_h]
+sanity_check_commands += ['%s --version' % x for x in _binaries_version]
+sanity_check_commands += ['%s -v' % x for x in _binaries_v]
+sanity_check_commands += ['%s 2>&1 | grep USAGE' % x for x in _binaries_helpless]
+
+modextrapaths = {
+    'PATH': 'scripts',
+    'PERL5LIB': 'scripts',
+}
+
+modextravars = {
+    'HHLIB': '%(installdir)s',
+}
+
+moduleclass = 'bio'

easybuild/easyconfigs/m/ModPipe/ModPipe-2.3.1-foss-2025b-Linux_x86_64.eb

@@ -0,0 +1,97 @@
+easyblock = 'PythonPackage'
+
+name = 'ModPipe'
+version = '2.3.1'
+versionsuffix = '-Linux_x86_64'
+_modeller_version = '10.7'
+
+homepage = 'https://salilab.org/modpipe'
+description = """
+ModPipe is a completely automated software pipeline that can calculate protein structure models for a large number
+of sequences with almost no manual intervention. In the simplest case, it takes as input a sequence identifier and
+a configuration file and produces one or more comparative models for that sequence.
+"""
+
+toolchain = {'name': 'foss', 'version': '2025b'}
+
+source_urls = ['https://salilab.org/modpipe/']
+sources = [
+    SOURCELOWER_TAR_GZ,
+    {
+        'source_urls': [f'https://salilab.org/modeller/{_modeller_version}/'],
+        'filename': f'modeller-{_modeller_version}.tar.gz',
+    },
+]
+checksums = [
+    {'modpipe-2.3.1.tar.gz': 'a006f436305d5f582f9ce461c73f8f02e1eb6fd416705276373697715209a4a6'},
+    {'modeller-10.7.tar.gz': 'b81ffee26841ef96470341889fa4af560f968cf35ef990d95480c7eb7a5b5c8f'},
+]
+
+dependencies = [
+    ('Perl', '5.40.2'),
+    ('Python', '3.13.5'),
+    ('GLib', '2.85.3'),
+    ('BLAST', '2.2.26', versionsuffix, SYSTEM),
+    ('HH-suite', '3.3.0-2025-08-12'),
+    ('PyYAML', '6.0.2'),
+]
+
+# Install Modeller-10.7 into the builddir of ModPipe - replace interactive install script
+# export MODELLER_LICENSE_KEY=your license key or this will fail
+_modeller_exe_version = '10v7'
+_modeller_installdir = '%(builddir)s/%(namelower)s-%(version)s/ext/mod'
+_modeller_builddir = f'%(builddir)s/modeller-{_modeller_version}'
+_cfg = f'{_modeller_installdir}/modlib/modeller/config.py'
+_modeller_install_cmds = (
+    f"mkdir -p {_modeller_installdir}/bin {_modeller_installdir}/lib && "
+    f"cd {_modeller_builddir} && cp -a README INSTALLATION doc examples modlib src {_modeller_installdir} && "
+    f"cd {_modeller_builddir}/bin && "
+    f"cp -a *.top lib mod{_modeller_version}_%(arch)s-intel8 {_modeller_installdir }/bin && "
+    f"cd {_modeller_builddir}/lib && cp -a %(arch)s-intel8 {_modeller_installdir}/lib && "
+    f"sed -e 's/EXECUTABLE_TYPE{_modeller_exe_version}=xxx/EXECUTABLE_TYPE{_modeller_exe_version}=%(arch)s-intel8/' "
+    rf"-e 's|MODINSTALL{_modeller_exe_version}=xxx|MODINSTALL{_modeller_exe_version}=\"{_modeller_installdir}\"|' "
+    f'{_modeller_builddir}/bin/modscript > {_modeller_installdir}/bin/mod{_modeller_version} && '
+    rf"sed -e 's|@TOPDIR@|\"{_modeller_installdir}\"|' -e 's/@EXETYPE@/%(arch)s-intel8/' "
+    f'{_modeller_builddir}/bin/modpy.sh.in > {_modeller_installdir}/bin/modpy.sh && '
+    f'chmod a+x {_modeller_installdir}/bin/mod{_modeller_version} {_modeller_installdir}/bin/modpy.sh && '
+    f'printf "%s\\n" "install_dir = \'{_modeller_installdir}\'" >> "{_cfg}" && '
+    """printf "%s\\n" "license = __import__('os').getenv('MODELLER_LICENSE_KEY', """
+    f"""'set MODELLER_LICENSE_KEY with your license key.')" > "{_cfg}" && """
+    f'cp %(builddir)s/%(namelower)s-%(version)s/ext/guess-arch.sh {_modeller_installdir}/bin/guess-arch.sh && '
+    "cd %(start_dir)s && "
+)
+
+# install by 'python setup.py'
+use_pip = False
+
+# the paths in scripts are changed during the python setup.py based on cwd
+buildininstalldir = True
+
+skipsteps = ['install']
+prebuildopts = _modeller_install_cmds
+# fix path of HHPaths.pm from HH-suite
+prebuildopts += (
+    "sed -i 's|lib/hh/scripts/HHPaths.pm|scripts/HHPaths.pm|' %(builddir)s/%(namelower)s-%(version)s/setup.py && "
+)
+buildcmd = '--with-blast=$EBROOTBLAST/bin --with-hhsuite=$EBROOTHHMINSUITE'
+
+# clean installdir
+postinstallcmds = [f"rm -r %(builddir)s/modeller-{_modeller_version}"]
+
+fix_perl_shebang_for = ['*.pl']
+fix_python_shebang_for = ['*.py']
+
+sanity_check_paths = {
+    'files': ['%(namelower)s-%(version)s/bin/%(namelower)s'],
+    'dirs': ['%(namelower)s-%(version)s/bin', '%(namelower)s-%(version)s/lib'],
+}
+
+sanity_check_commands = ['%(namelower)s help']
+
+modextrapaths = {
+    'PATH': '%(namelower)s-%(version)s/bin',
+    'PERL5LIB': '%(namelower)s-%(version)s/lib/perl',
+    'PYTHONPATH': '%(namelower)s-%(version)s/lib/python'
+}
+
+moduleclass = 'tools'