Merge pull request #21387 from boegel/20240912170535_new_pr_BiG-SCAPE119

{bio}[foss/2023b] BiG-SCAPE v1.1.9, HMMER v3.4, FastTree v2.1.11

easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.9-foss-2023b.eb

@@ -0,0 +1,68 @@
+easyblock = 'PythonPackage'
+
+name = 'BiG-SCAPE'
+version = '1.1.9'
+
+homepage = 'https://bigscape-corason.secondarymetabolites.org/index.html'
+description = """BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters 
+(BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene 
+cluster families, and exploring gene cluster diversity linked to enzyme phylogenies."""
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+
+github_account = 'medema-group'
+source_urls = [GITHUB_SOURCE]
+sources = ['v%(version)s.tar.gz']
+patches = [
+    'BiG-SCAPE-1.1.5_use_env_var_for_html.patch',
+    'BiG-SCAPE-1.1.5_use_correct_name_for_FastTree.patch',
+]
+checksums = [
+    {'v1.1.9.tar.gz': 'ef0ddb5b433e0b1467ae5f96037fd6d23ebcba6bc08201d1421eba35d072e534'},
+    {'BiG-SCAPE-1.1.5_use_env_var_for_html.patch': '540be22396ab982c2aeaaed4ce5acdb8ccb8ce2b31d36bc69d37be7a29c7c42a'},
+    {'BiG-SCAPE-1.1.5_use_correct_name_for_FastTree.patch':
+     'e1572e4134c6163a3927ac32bd2a39b7f87cf01109f7913b3c55126e2381a771'},
+]
+
+dependencies = [
+    ('Python', '3.11.5'),
+    ('SciPy-bundle', '2023.11'),
+    ('Biopython', '1.84'),
+    ('scikit-learn', '1.4.0'),
+    ('networkx', '3.2.1'),
+    ('HMMER', '3.4'),
+    ('FastTree', '2.1.11'),
+]
+
+use_pip = True
+download_dep_fail = True
+sanity_pip_check = True
+
+options = {'modulename': 'bigscape'}
+
+local_lib_py_bigscape_path = 'lib/python%(pyshortver)s/site-packages/bigscape'
+
+sanity_check_paths = {
+    'files': ['bin/bigscape'],
+    'dirs': [local_lib_py_bigscape_path],
+}
+
+sanity_check_commands = [
+    'bigscape --help',
+]
+
+modextravars = {
+    'BIG_SCAPE_HTML_PATH': '%(installdir)s/' + local_lib_py_bigscape_path,
+}
+
+modloadmsg = "%(name)s needs processed Pfam database to work properly.\n"
+modloadmsg += "For this, download the latest 'Pfam-A.hmm.gz' file from the Pfam website "
+modloadmsg += "(http://ftp.ebi.ac.uk/pub/databases/Pfam/releases/), "
+modloadmsg += "uncompress it and process it using the `hmmpress` command.\n"
+modloadmsg += "For data files, like the domains_color_file.tsv and domain_includelist.txt, "
+modloadmsg += "one can set the environment variable BIG_SCAPE_DATA_PATH, if that is not set "
+modloadmsg += "it will use the directory where the bigscape command is started from.\n"
+modloadmsg += "One can copy the domains_color_file.tsv from "
+modloadmsg += "%(installdir)s/lib/python%(pyshortver)s/site-packages/BiG-SCAPE/domains_color_file.tsv\n"
+
+moduleclass = 'bio'

easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-13.2.0.eb

@@ -0,0 +1,42 @@
+# Updated from previous config
+# Author: Pavel Grochal (INUITS)
+# License: GPLv2
+
+easyblock = 'CmdCp'
+
+name = 'FastTree'
+version = '2.1.11'
+
+homepage = 'http://www.microbesonline.org/fasttree/'
+description = """FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide
+ or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of
+ time and memory. """
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+toolchainopts = {'openmp': True}
+
+# HTTPS cert error:
+# hostname 'www.microbesonline.org' doesn't match either of 'genomics.lbl.gov', 'mojave.qb3.berkeley.edu', ...
+source_urls = ['http://www.microbesonline.org/fasttree/']
+sources = [{'filename': '%(name)s-%(version)s.c', 'extract_cmd': 'cp %s FastTree.c'}]
+checksums = ['9026ae550307374be92913d3098f8d44187d30bea07902b9dcbfb123eaa2050f']
+
+builddependencies = [('binutils', '2.40')]
+
+cmds_map = [('%(name)s-%(version)s.c', '$CC -DOPENMP $CFLAGS $LIBS %%(source)s -o %(name)s')]
+
+files_to_copy = [(['FastTree'], 'bin')]
+
+# as FastTree is built with OpenMP, the correct binary is FastTreeMP
+# the FastTree binary should normally be built without OpenMP, but let’s keep it as is for backward compatibility
+# see http://www.microbesonline.org/fasttree/#OpenMP
+postinstallcmds = ['cd %(installdir)s/bin && ln -s FastTree FastTreeMP']
+
+sanity_check_paths = {
+    'files': ['bin/FastTree'],
+    'dirs': [],
+}
+
+sanity_check_commands = ['FastTree 2>&1 | grep "FastTree Version %(version)s"']
+
+moduleclass = 'bio'

easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2023b.eb

@@ -0,0 +1,78 @@
+##
+# EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+#
+# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA
+# Authors::   Nils Christian <[email protected]>,
+#             Fotis Georgatos <[email protected]>
+# Updated by: Filip Kružík (INUITS)
+# 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
+##
+
+easyblock = 'ConfigureMake'
+
+name = 'HMMER'
+version = '3.4'
+
+homepage = 'http://hmmer.org/'
+description = """HMMER is used for searching sequence databases for homologs
+ of protein sequences, and for making protein sequence alignments. It
+ implements methods using probabilistic models called profile hidden Markov
+ models (profile HMMs).  Compared to BLAST, FASTA, and other sequence
+ alignment and database search tools based on older scoring methodology,
+ HMMER aims to be significantly more accurate and more able to detect remote
+ homologs because of the strength of its underlying mathematical models. In the
+ past, this strength came at significant computational expense, but in the new
+ HMMER3 project, HMMER is now essentially as fast as BLAST."""
+
+toolchain = {'name': 'gompi', 'version': '2023b'}
+
+source_urls = [
+    'http://eddylab.org/software/hmmer/',
+    'http://eddylab.org/software/hmmer%(version_major)s/%(version)s/',
+]
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['ca70d94fd0cf271bd7063423aabb116d42de533117343a9b27a65c17ff06fbf3']
+
+builddependencies = [
+    ('Python', '3.11.5'),
+    ('Perl', '5.38.0'),
+]
+
+# replace hardcoded /usr/bin/perl shebang lines with '/usr/bin/env perl' across all files
+preconfigopts = "grep '/usr/bin/perl' . | cut -f1 -d: | xargs echo sed -i 's@/usr/bin/perl@/usr/bin/env perl@g' && "
+
+configopts = '--enable-mpi'
+
+buildopts = ' V=1 '
+
+testopts = buildopts
+runtest = 'check'
+
+installopts = ' && cd easel && make install'
+
+local_bin_files = ['alimask', 'esl-afetch', 'esl-alimanip', 'esl-alimap', 'esl-alimask',
+                   'esl-alimerge', 'esl-alipid', 'esl-alirev', 'esl-alistat', 'esl-compalign',
+                   'esl-compstruct', 'esl-construct', 'esl-histplot', 'esl-mask', 'esl-reformat',
+                   'esl-selectn', 'esl-seqrange', 'esl-seqstat', 'esl-sfetch', 'esl-shuffle',
+                   'esl-ssdraw', 'esl-translate', 'esl-weight', 'hmmalign', 'hmmbuild',
+                   'hmmconvert', 'hmmemit', 'hmmfetch', 'hmmlogo', 'hmmpgmd', 'hmmpress',
+                   'hmmscan', 'hmmsearch', 'hmmsim', 'hmmstat', 'jackhmmer', 'makehmmerdb',
+                   'nhmmer', 'nhmmscan', 'phmmer']
+
+sanity_check_paths = {
+    'files': ["bin/%s" % x for x in local_bin_files],
+    'dirs': ['bin', 'share'],
+}
+
+sanity_check_commands = [
+    "esl-construct -h",
+    "hmmsearch -h",
+    "nhmmer -h",
+]
+
+moduleclass = 'bio'