{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-3.3.0-20250812-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 = '3.3.0-20250812'
+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'
+
+# some software that requires HH-suite (like ModPipe) looks for script in lib/hh/scripts
+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.eb

@@ -0,0 +1,96 @@
+easyblock = 'Bundle'
+
+name = 'ModPipe'
+version = '2.3.1'
+_modeller_version = '10.7'
+_blast_version = '2.2.26'
+
+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'}
+
+build_info_msg = """
+Set KEY_MODELLER environment variable to the MODELLER key before running the
+installer. The key can be obtained from the MODELLER website:
+https://salilab.org/modeller/registration.html
+"""
+
+dependencies = [
+    ('Perl', '5.40.2'),
+    ('Python', '3.13.5'),
+    ('GLib', '2.85.3'),
+    ('HH-suite', '3.3.0-20250812'),
+    ('PyYAML', '6.0.2'),
+]
+
+# fix path of HHPaths.pm from HH-suite
+_mp_prebuildopts = (
+    "sed -i 's|lib/hh/scripts/HHPaths.pm|scripts/HHPaths.pm|' %(builddir)s/%(namelower)s-%(version)s/setup.py && "
+)
+
+# run Install script to install Modeller into ModPipe
+# https://salilab.org/modpipe/doc/install-ext.html#modeller
+_modeller_install_cmd = 'cd %(builddir)s/%(namelower)s-%(version)s && '
+_modeller_install_cmd += f'MODINSTALL=%(builddir)s/modpipe-{version}/ext/mod ./Install'
+
+components = [
+    ('BLAST', _blast_version, {
+        'easyblock': 'Tarball',
+        'install_type': 'subdir',
+        'source_urls': ['https://ftp.ncbi.nlm.nih.gov/blast/executables/legacy.NOTSUPPORTED/%(version)s/'],
+        'sources': ['%(namelower)s-%(version)s-x64-linux.tar.gz'],
+        'checksums': ['8a2f986cf47f0f7cbdb3478c4fc7e25c7198941d2262264d0b6b86194b3d063d'],
+    }),
+    ('Modeller', _modeller_version, {
+        'easyblock': 'Binary',
+        'source_urls': [f'https://salilab.org/modeller/{_modeller_version}/'],
+        'sources': [f'modeller-{_modeller_version}.tar.gz'],
+        'patches': ['Modeller-10.7_install-to-modpipe.patch'],
+        'install_cmd': _modeller_install_cmd,
+        'checksums': [
+            'b81ffee26841ef96470341889fa4af560f968cf35ef990d95480c7eb7a5b5c8f',  # modeller-10.7.tar.gz
+            '5d50805f40436dcdec879b088bf5654b288c9a7d593b74df70792e46acfd903f',  # install-to-modpipe.patch
+        ],
+    }),
+    (name, version, {
+        'easyblock': 'PythonPackage',
+        'source_urls': ['https://salilab.org/modpipe/'],
+        'sources': [SOURCELOWER_TAR_GZ],
+        'start_dir': '%(namelower)s-%(version)s',
+        # install by 'python setup.py --with-blast=... --with-hhsuite=...'
+        'use_pip': False,
+        'skipsteps': ['install'],
+        'prebuildopts': _mp_prebuildopts,
+        'buildcmd': f'--with-blast=%(installdir)s/blast-{_blast_version}/bin --with-hhsuite=$EBROOTHHMINSUITE',
+        'checksums': ['a006f436305d5f582f9ce461c73f8f02e1eb6fd416705276373697715209a4a6'],
+    })
+]
+
+# paths in scripts are changed during the installation based on cwd
+buildininstalldir = True
+
+# cleanup duplicated blast dir
+postinstallcmds = ['rm -r %(installdir)s/blast']
+
+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'

easybuild/easyconfigs/m/ModPipe/Modeller-10.7_install-to-modpipe.patch

@@ -0,0 +1,64 @@
+Change Install script to run noninteractively using environment variables + install Modeller to ModPipe
+Author: Samuel Moors (Vrije Universiteit Brussel)
+Update for ModPipe: Pavel Tomanek (Inuits)
+
+--- modeller-10.7/Install.orig	2025-09-04 15:20:51.390000000 +0200
++++ modeller-10.7/Install	2025-09-17 13:59:29.814302000 +0200
+@@ -71,11 +71,8 @@
+ echo '   5) Linux on 64-bit ARM (e.g. for Raspberry Pi 3 or later).'
+ echo
+ printf "Select the type of your computer from the list above [$DEFexectype]: "
+-read ans
+-if [ x$ans != x ] ; then
+-  exectype=$ans
+-else
+-  exectype=$DEFexectype
++if [[ -z $exectype ]]; then
++    exectype=$DEFexectype
+ fi
+ if [ $exectype = 1 ] ; then EXECUTABLE_TYPE=$exectype1 ; fi
+ if [ $exectype = 2 ] ; then EXECUTABLE_TYPE=$exectype2 ; fi
+@@ -88,10 +85,7 @@
+ echo
+ echo "Full directory name in which to install $MOD"
+ printf "[$DEFmodinstall]: "
+-read ans
+-if [ x$ans != x ] ; then 
+-   MODINSTALL=$ans
+-else
++if [[ -z $MODINSTALL ]]; then
+    MODINSTALL=$DEFmodinstall
+ fi
+ if [ ! -d $MODINSTALL ] ; then
+@@ -103,7 +97,6 @@
+ echo
+ echo "License key, obtained from our academic license server at"
+ printf "https://salilab.org/modeller/registration.html: "
+-read KEY_MODELLER
+
+
+ echo
+@@ -118,7 +111,6 @@
+ echo "If they are incorrect, abort installation (ctrl-c) and run Install again."
+ echo
+ printf "Press <Enter> to begin the installation: "
+-read ans
+ echo
+ echo "------------------------------------------------------------------------"
+ echo
+@@ -153,7 +145,6 @@
+ echo "license = '${KEY_MODELLER}'" >> ${config}
+ echo "Installation complete."
+ printf "Press <Enter> to continue: "
+-read ans
+
+ echo
+ echo "------------------------------------------------------------------------"
+@@ -180,7 +171,6 @@
+ echo "------------------------------------------------------------------------"
+ echo
+ printf "Press <Enter> to continue: "
+-read ans
+
+ echo
+ echo "------------------------------------------------------------------------"