Merge pull request easybuilders#21120 from SebastianAchilles/20240804…

…172613_new_pr_BioPerl178

{data,tools}[GCCcore/13.3.0] BioPerl v1.7.8, DB v18.1.40, DB_File v1.859, ...

easybuild/easyconfigs/a/attr/attr-2.5.2-GCCcore-13.3.0.eb

@@ -0,0 +1,28 @@
+easyblock = 'ConfigureMake'
+
+name = 'attr'
+version = '2.5.2'
+
+homepage = 'https://savannah.nongnu.org/projects/attr'
+
+description = """Commands for Manipulating Filesystem Extended Attributes"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = [GNU_SAVANNAH_SOURCE]
+sources = [SOURCE_TAR_GZ]
+checksums = ['39bf67452fa41d0948c2197601053f48b3d78a029389734332a6309a680c6c87']
+
+builddependencies = [('binutils', '2.42')]
+
+sanity_check_paths = {
+    'files': ['bin/attr', 'bin/getfattr', 'bin/setfattr',
+              'include/%(name)s/attributes.h', 'include/%(name)s/error_context.h',
+              'include/%(name)s/libattr.h', 'lib/libattr.a',
+              'lib/libattr.%s' % SHLIB_EXT],
+    'dirs': ['share'],
+}
+
+sanity_check_commands = ["getfattr --help"]
+
+moduleclass = 'tools'

easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-13.3.0.eb

@@ -0,0 +1,58 @@
+# easybuild easyconfig
+#
+#  John Dey [email protected]
+#
+#  Fred Hutchinson Cancer Research Center
+#  Thomas Eylenbosch - Gluo NV 
+
+easyblock = 'PerlModule'
+
+name = 'BioPerl'
+version = '1.7.8'
+
+homepage = 'https://bioperl.org/'
+description = """Bioperl is the product of a community effort to produce Perl code which is useful in biology.
+ Examples include Sequence objects, Alignment objects and database searching objects."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+builddependencies = [('binutils', '2.42')]
+
+dependencies = [
+    ('Perl', '5.38.2'),
+    ('Perl-bundle-CPAN', '5.38.2'),
+    ('XML-LibXML', '2.0210'),
+    ('DB_File', '1.859'),
+]
+
+exts_defaultclass = 'PerlModule'
+exts_filter = ("perldoc -lm %(ext_name)s ", "")
+
+exts_list = [
+    ('XML::Writer', '0.900', {
+        'source_tmpl': 'XML-Writer-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/J/JO/JOSEPHW'],
+        'checksums': ['73c8f5bd3ecf2b350f4adae6d6676d52e08ecc2d7df4a9f089fa68360d400d1f'],
+    }),
+    (name, version, {
+        'source_tmpl': '%(name)s-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'],
+        'checksums': ['c490a3be7715ea6e4305efd9710e5edab82dabc55fd786b6505b550a30d71738'],
+    }),
+    ('Bio::Procedural', '1.7.4', {
+        'source_tmpl': 'Bio-Procedural-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'],
+        'checksums': ['d2bd9cfbb091eee2d80ed6cf812ac3813b1c8a1aaca20671037f5f225d31d1da'],
+    }),
+]
+
+modextrapaths = {
+    'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/',
+}
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['bin', 'lib/perl5/site_perl/%(perlver)s/Bio'],
+}
+
+moduleclass = 'bio'

easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-13.3.0.eb

@@ -0,0 +1,33 @@
+name = 'DB'
+version = '18.1.40'
+
+homepage = 'https://www.oracle.com/technetwork/products/berkeleydb'
+
+description = """Berkeley DB enables the development of custom data management
+ solutions, without the overhead traditionally associated with such custom
+ projects."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+# use http to allow auto-downloading...
+source_urls = ['http://download.oracle.com/berkeley-db/']
+sources = [SOURCELOWER_TAR_GZ]
+patches = ['%(name)s-%(version)s_fix_doc_install.patch']
+checksums = [
+    '0cecb2ef0c67b166de93732769abdeba0555086d51de1090df325e18ee8da9c8',  # db-18.1.40.tar.gz
+    '441f48568156f72f02a8662998d293cc7edad687604b4f8af722f21c6db2a52d',  # DB-18.1.40_fix_doc_install.patch
+]
+
+builddependencies = [('binutils', '2.42')]
+
+dependencies = [('OpenSSL', '3', '', SYSTEM)]
+
+sanity_check_paths = {
+    'files': ['bin/db_%s' % x for x in ['archive', 'checkpoint', 'convert', 'deadlock', 'dump', 'hotbackup',
+                                        'load', 'log_verify', 'printlog', 'recover', 'replicate', 'stat',
+                                        'tuner', 'upgrade', 'verify']] +
+             ['include/db.h', 'lib/libdb.a', 'lib/libdb.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'tools'

easybuild/easyconfigs/d/DB_File/DB_File-1.859-GCCcore-13.3.0.eb

@@ -0,0 +1,31 @@
+easyblock = 'PerlModule'
+
+name = 'DB_File'
+version = '1.859'
+
+homepage = 'https://perldoc.perl.org/DB_File.html'
+description = """Perl5 access to Berkeley DB version 1.x."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['https://www.cpan.org/modules/by-module/DB_File/PMQS']
+sources = [SOURCE_TAR_GZ]
+checksums = ['5674e0d2cd0b060c4d1253670ea022c64d842a55257f9eb8edb19c0f53e2565c']
+
+builddependencies = [
+    ('binutils', '2.42'),
+]
+
+dependencies = [
+    ('Perl', '5.38.2'),
+    ('DB', '18.1.40'),
+]
+
+preconfigopts = 'env DB_FILE_INCLUDE="$EBROOTDB/include" DB_FILE_LIB="$EBROOTDB/lib" '
+
+sanity_check_paths = {
+    'files': ['lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/DB_File.pm'],
+    'dirs': [],
+}
+
+moduleclass = 'data'

easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0210-GCCcore-13.3.0.eb

@@ -0,0 +1,65 @@
+# updated toolchain, version, and dependency versions
+# Thomas Eylenbosch 5-Jun-23
+
+easyblock = 'Bundle'
+
+name = 'XML-LibXML'
+version = '2.0210'
+
+homepage = 'https://metacpan.org/pod/distribution/XML-LibXML/LibXML.pod'
+description = "Perl binding for libxml2"
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('pkgconf', '2.2.0'),
+]
+
+dependencies = [
+    ('Perl', '5.38.2'),
+    ('Perl-bundle-CPAN', '5.38.2'),
+    ('libxml2', '2.12.7'),
+]
+
+exts_defaultclass = 'PerlModule'
+exts_filter = ("perldoc -lm %(ext_name)s ", "")
+
+exts_list = [
+    ('File::chdir', '0.1011', {
+        'source_tmpl': 'File-chdir-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'],
+        'checksums': ['31ebf912df48d5d681def74b9880d78b1f3aca4351a0ed1fe3570b8e03af6c79'],
+    }),
+    ('Alien::Base', '2.83', {
+        'source_tmpl': 'Alien-Build-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE/'],
+        'checksums': ['4817270314431350ff397125547f55641dcff98bdde213b9e5efc613f7c8b85a'],
+    }),
+    ('Alien::Build::Plugin::Download::GitLab', '0.01', {
+        'source_tmpl': 'Alien-Build-Plugin-Download-GitLab-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'],
+        'checksums': ['c1f089c8ea152a789909d48a83dbfcf2626f773daf30431c8622582b26aba902'],
+    }),
+    ('Alien::Libxml2', '0.19', {
+        'source_tmpl': 'Alien-Libxml2-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'],
+        'checksums': ['f4a674099bbd5747c0c3b75ead841f3b244935d9ef42ba35368024bd611174c9'],
+    }),
+    ('XML::LibXML', version, {
+        'source_tmpl': 'XML-LibXML-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF/'],
+        'checksums': ['a29bf3f00ab9c9ee04218154e0afc8f799bf23674eb99c1a9ed4de1f4059a48d'],
+    }),
+]
+
+modextrapaths = {
+    'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/',
+}
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/XML/LibXML'],
+}
+
+moduleclass = 'data'