Add easyconfig Bio-DB-HTS-3.01-GCC-13.2.0.eb

easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-13.2.0.eb

@@ -0,0 +1,32 @@
+easyblock = 'PerlModule'
+
+name = 'Bio-DB-HTS'
+version = '3.01'
+
+homepage = 'https://metacpan.org/release/Bio-DB-HTS'
+description = "Read files using HTSlib including BAM/CRAM, Tabix and BCF database files"
+
+toolchain = {'name': 'GCC', 'version': '13.2.0'}
+
+source_urls = ['https://cpan.metacpan.org/authors/id/A/AV/AVULLO/']
+sources = ['Bio-DB-HTS-%(version)s.tar.gz']
+checksums = ['12a6bc1f579513cac8b9167cce4e363655cc8eba26b7d9fe1170dfe95e044f42']
+
+builddependencies = [('pkgconf', '2.0.3')]
+
+dependencies = [
+    ('Perl', '5.38.0'),
+    ('BioPerl', '1.7.8'),
+    ('HTSlib', '1.19.1'),
+]
+
+preconfigopts = "env HTSLIB_DIR=$EBROOTHTSLIB"
+
+options = {'modulename': 'Bio::DB::HTS'}
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/perl5/site_perl/%(perlver)s', 'man/man3'],
+}
+
+moduleclass = 'bio'

easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-13.2.0.eb

@@ -0,0 +1,58 @@
+# easybuild easyconfig
+#
+#  John Dey [email protected]
+#
+#  Fred Hutchinson Cancer Research Center
+#  Thomas Eylenbosch - Gluo NV 
+
+easyblock = 'Bundle'
+
+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': '13.2.0'}
+
+builddependencies = [('binutils', '2.40')]
+
+dependencies = [
+    ('Perl', '5.38.0'),
+    ('Perl-bundle-CPAN', '5.38.0'),
+    ('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-13.2.0.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': '13.2.0'}
+
+# 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', '2.40')]
+
+dependencies = [('OpenSSL', '1.1', '', 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-13.2.0.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': '13.2.0'}
+
+source_urls = ['https://www.cpan.org/modules/by-module/DB_File/PMQS']
+sources = [SOURCE_TAR_GZ]
+checksums = ['5674e0d2cd0b060c4d1253670ea022c64d842a55257f9eb8edb19c0f53e2565c']
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+
+dependencies = [
+    ('Perl', '5.38.0'),
+    ('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/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb

@@ -2061,11 +2061,13 @@ exts_list = [
         'checksums': ['3973ebdc44682c9c15c776f66e8be242cb4ff1dd52caf43ff446b74d4dccca06'],
     }),
     ('Sys::Info::Driver::Linux::Device::CPU', '0.7905', {
+        'runtest': False,  # Fragile tests, specifically it fails on Debian systems
         'source_tmpl': 'Sys-Info-Driver-Linux-%(version)s.tar.gz',
         'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK'],
         'checksums': ['899c329bd3508ec5849ad0e5dadfa7c3679bbacaea9dda12404a7893032e8b7b'],
     }),
     ('Sys::Info', '0.7811', {
+        'runtest': False,  # Fragile tests, specifically it fails on Debian systems
         'source_tmpl': 'Sys-Info-%(version)s.tar.gz',
         'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK'],
         'checksums': ['566482bff3427c198d7955468ed945a8e736c4a2925151fdef96801ef8a401e1'],
@@ -2111,6 +2113,7 @@ exts_list = [
         'checksums': ['02408843c8e36ea3d507e9f33fee48d6908543829ebe320f13d1bfe76af31e09'],
     }),
     ('Sys::Info::Driver::Linux', '0.7905', {
+        'runtest': False,  # Fragile tests, specifically it fails on Debian systems
         'source_tmpl': 'Sys-Info-Driver-Linux-%(version)s.tar.gz',
         'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK'],
         'checksums': ['899c329bd3508ec5849ad0e5dadfa7c3679bbacaea9dda12404a7893032e8b7b'],