readd deleted easyconfig

Author: Samuel Moors

easybuild/easyconfigs/r/RepeatModeler/RepeatModeler-2.0.7-foss-2024a.eb

@@ -0,0 +1,69 @@
+easyblock = 'Tarball'
+
+name = 'RepeatModeler'
+version = '2.0.7'
+
+homepage = 'https://www.repeatmasker.org/'
+description = """RepeatModeler is a de novo transposable element (TE) family identification and modeling package. """
+
+toolchain = {'name': 'foss', 'version': '2024a'}
+
+github_account = 'Dfam-consortium'
+source_urls = [GITHUB_SOURCE]
+sources = ['%(version)s.tar.gz']
+checksums = ['2873697a885e7115bf5e940cf880f47de17efb7a200ec2d3a1627d5a689f7a8f']
+
+dependencies = [
+    ('Perl', '5.38.2'),
+    ('TRF', '4.09.1'),
+    ('RMBlast', '2.14.1'),
+    ('RepeatMasker', '4.2.1'),
+    ('RepeatScout', '1.0.7'),
+    ('RECON', '1.08'),
+    ('Kent_tools', '479'),
+    ('CD-HIT', '4.8.1'),
+    # Optional (required for LTR pipeline):
+    ('MAFFT', '7.526', '-with-extensions'),
+    ('GenomeTools', '1.6.5'),   # for LTRHarvest
+    ('LTR_retriever', '2.9.0'),  # see issue https://github.com/Dfam-consortium/RepeatModeler/issues/257
+    ('TWL-NINJA', '1.00-cluster_only'),
+]
+
+_tmpl = "\"/'%s' =>/,/'value' => '/s|'value' =>.*|'value' => '%s'|\""
+
+postinstallcmds = [
+    ' '.join([
+        'sed -i',
+        '-e', _tmpl % ('CDHIT_DIR', '$EBROOTCDMINHIT/bin'),
+        '-e', _tmpl % ('GENOMETOOLS_DIR', '$EBROOTGENOMETOOLS/bin'),
+        '-e', _tmpl % ('LTR_RETRIEVER_DIR', '$EBROOTLTR_RETRIEVER'),
+        '-e', _tmpl % ('MAFFT_DIR', '$EBROOTMAFFT/bin'),
+        '-e', _tmpl % ('NINJA_DIR', '$EBROOTTWLMINNINJA/bin'),
+        '-e', _tmpl % ('RECON_DIR', '$EBROOTRECON/bin'),
+        '-e', _tmpl % ('REPEATMASKER_DIR', '$EBROOTREPEATMASKER'),
+        '-e', _tmpl % ('RMBLAST_DIR', '$EBROOTRMBLAST/bin'),
+        '-e', _tmpl % ('RSCOUT_DIR', '$EBROOTREPEATSCOUT'),
+        '-e', _tmpl % ('TRF_DIR', '$EBROOTTRF/bin'),
+        '-e', _tmpl % ('UCSCTOOLS_DIR', '$EBROOTKENT_TOOLS/bin'),
+        '%(installdir)s/RepModelConfig.pm',
+    ]),
+]
+
+_bins = ['BuildDatabase', 'LTRPipeline', 'Refiner', 'RepeatClassifier', 'RepeatModeler', 'TRFMask',
+         'util/CntSubst', 'util/Linup']
+
+fix_perl_shebang_for = _bins + ['util/*.pl']
+
+modextrapaths = {
+    'PATH': '',
+    'PERL5LIB': '',
+}
+
+sanity_check_paths = {
+    'files': _bins + ['Job.pm', 'RepeatUtil.pm', 'RepModelConfig.pm'],
+    'dirs': ['Libraries', 'Matrices', 'util'],
+}
+
+sanity_check_commands = ["RepeatModeler -help | grep 'RepeatModeler - Model repetitive DNA'"]
+
+moduleclass = 'bio'