From 531f4e9003bbd3d1797426afc46e3639dbaf0f01 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Thu, 17 Oct 2024 12:19:42 +0200
Subject: [PATCH] #435 working cisDIV

---
 435_cisDiversity/cisDiv.eb | 96 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 96 insertions(+)
 create mode 100644 435_cisDiversity/cisDiv.eb

diff --git a/435_cisDiversity/cisDiv.eb b/435_cisDiversity/cisDiv.eb
new file mode 100644
index 0000000..f929ff6
--- /dev/null
+++ b/435_cisDiversity/cisDiv.eb
@@ -0,0 +1,96 @@
+easyblock = 'MakeCp'
+
+name = 'cisDIVERSITY'
+version = '1.1'
+
+homepage = 'https://github.com/NarlikarLab/cisDIVERSITY/'
+description = """A module discovery tool used for finding diverse sequence architectures, 
+each one characterized by presence or absence of de novo motifs."""
+
+toolchain = {'name': 'foss', 'version': '2020a'}
+
+source_urls = ['https://github.com/NarlikarLab/cisDIVERSITY/releases/download/v%(version)s/']
+sources = [{
+    'download_filename': '%(name)s_v%(version)s.tar.gz',
+    'filename': SOURCE_TAR_GZ,
+}]
+checksums = ['4ba5967fa754ec78b9dd6b6dc9d2ee5de87dbb4d7906d47e57e73aec87897725']
+
+# builddependencies = [('patchelf', '0.18.0')]
+dependencies = [
+    ('Python', '2.7.18'),
+    ('SciPy-bundle', '2020.03', '-Python-%(pyver)s'),
+    ('R', '3.6.3'),
+]
+
+# exts_defaultclass = 'PythonPackage'
+# exts_default_options = {
+#     'source_urls': [PYPI_SOURCE],
+#     'download_dep_fail': True,
+#     'use_pip': True,
+#     'sanity_pip_check': True,
+#     'preinstallopts': '',
+#     'installopts': '',
+# }
+
+# exts_list = [
+#     ('Paralleltask', '0.2.3', {
+#         'modulename': 'paralleltask',
+#         'checksums': ['8015a8311d5021bc44edbfbf45ff2557a529999e235d25190bac62993fdf7b66'],
+#     }),
+# ]
+
+# # fix make -C util - warning: jobserver unavailable
+# parallel = 1
+
+# # fix bwa bug - https://github.com/Nextomics/NextPolish/issues/83
+# # + use SAMtools and minimap2 from EB
+# prebuildopts = "sed -i 's/seq_count bwa samtools minimap2/seq_count/' Makefile && "
+# prebuildopts += "rm -rf util/bwa && rm -fr util/minimap2 && rm -rf util/samtools && "
+# prebuildopts += (
+#     "sed -i"
+#     " -e 's/seq_split seq_count bwa_ samtools_ minimap2_/seq_split seq_count/'"
+#     " -e '/BWADIR/d'"
+#     " -e '/bwa_:/d'"
+#     " -e '/SAMTOOLSDIR/d'"
+#     " -e '/MINIMAP2DIR/d'"
+#     " -e '/samtools_:/d'"
+#     " -e '/minimap2_:/d'"
+#     " util/Makefile && "
+# )
+# postinstallcmds = [
+#     # links to binaries
+#     "cd %(installdir)s/bin && ln -s $EBROOTBWA/bin/bwa && "
+#     "ln -s $EBROOTSAMTOOLS/bin/samtools && ln -s $EBROOTMINIMAP2/bin/minimap2",
+#     # set RPATH to calgs.so, nextpolish1.so and nextpolish2.so
+#     "if %(rpath_enabled)s; then "
+#     "patchelf --force-rpath --set-rpath '$ORIGIN:$ORIGIN/../lib'"
+#     '":$EBROOTZLIB/lib" %(installdir)s/lib/calgs.so && '
+#     "patchelf --force-rpath --set-rpath '$ORIGIN:$ORIGIN/../lib'"
+#     '"$EBROOTZLIB/lib:$EBROOTBZIP2/lib:$EBROOTXZ/lib" %(installdir)s/lib/nextpolish1.so && '
+#     "patchelf --force-rpath --set-rpath '$ORIGIN:$ORIGIN/../lib'"
+#     '"$EBROOTZLIB/lib:$EBROOTBZIP2/lib:$EBROOTXZ/lib" %(installdir)s/lib/nextpolish2.so; fi',
+# ]
+
+# files_to_copy = ['bin', 'lib', 'test_data', 'LICENSE', 'nextPolish']
+# files_to_copy = ['*']
+files_to_copy = [(['learnDiverseModules'], 'bin')]
+
+sanity_check_paths = {
+    'files': ['bin/learnDiverseModules'],
+    'dirs': [],
+}
+
+sanity_check_commands = ['learnDiverseModules -h']
+
+# modextrapaths = {
+#     'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages',
+#     'PATH': '',
+# }
+
+moduleclass = 'bio'
+
+# builddir:
+    # /tmp/vsc47063/easybuild/build/cisDIVERSITY/1.1/foss-2020a
+# installdir:
+    # scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/cisDIVERSITY/1.1-foss-2020a
\ No newline at end of file