Merge pull request easybuilders#19594 from smoors/20240116120331_new_…

…pr_rMATS-turbo420 {bio}[gfbf/2023a] rMATS-turbo v4.2.0
SimonPinches · Jan 16, 2024 · 31c44de · 31c44de
2 parents 6078069 + 70ed1fe
commit 31c44de
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diff --git a/easybuild/easyconfigs/r/rMATS-turbo/rMATS-turbo-4.2.0-gfbf-2023a.eb b/easybuild/easyconfigs/r/rMATS-turbo/rMATS-turbo-4.2.0-gfbf-2023a.eb
@@ -0,0 +1,70 @@
+easyblock = 'Bundle'
+
+name = 'rMATS-turbo'
+version = '4.2.0'
+
+homepage = 'https://github.com/Xinglab/rmats-turbo'
+description = """rMATS turbo is the C/Cython version of rMATS (refer to https://rnaseq-mats.sourceforge.io)."""
+
+toolchain = {'name': 'gfbf', 'version': '2023a'}
+toolchainopts = {'openmp': True}
+
+builddependencies = [
+    ('CMake', '3.26.3'),
+]
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('GSL', '2.7'),
+    ('SAMtools', '1.18'),
+    ('STAR', '2.7.11a'),
+    ('BamTools', '2.5.2'),
+]
+
+local_ldflags = " -lm -lgsl -lgslcblas $LIBLAPACK"
+local_buildopts = '  CC="$CC" CXX="$CXX" FC="$FC" LDFLAGS="%s"' % local_ldflags
+
+default_component_specs = {
+    'sources': ['v%(version)s.tar.gz'],
+    'source_urls': ['https://github.com/Xinglab/%(name)s/archive/refs/tags/'],
+    'checksums': ['80fd32ffa00190b2eb3fcefcd4efb0d466a808c5e80bc91419a71bc033cdbd72'],
+}
+
+components = [
+    (name, version, {
+        'easyblock': 'MakeCp',
+        'start_dir': 'rmats-turbo-%(version)s/rMATS_C',
+        'buildopts': "%s" % local_buildopts,
+        'files_to_copy': [(['rMATSexe', '../rmats.py', '../rMATS_C', '../rMATS_R', '../rMATS_P'], 'bin')]
+    }),
+    ('rmats-turbo-python', version, {
+        'easyblock': 'PythonPackage',
+        'patches': ['rMATS-turbo-%(version)s_bamtools_as_dependency.patch'],
+        'checksums': [
+            '80fd32ffa00190b2eb3fcefcd4efb0d466a808c5e80bc91419a71bc033cdbd72',
+            'a4c70e3d8ef9723fcb801d39a62c132f8f1903fb3a60dad330de895c12f5f7e7',
+        ],
+        'start_dir': 'rmats-turbo-%(version)s/rMATS_pipeline',
+        'use_pip': True,
+        'download_dep_fail': True,
+        'sanity_pip_check': True,
+        'options': {'modulename': 'rmatspipeline'},
+    }),
+]
+
+modextrapaths = {
+    'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']
+}
+
+postinstallcmds = ["chmod a+x %(installdir)s/bin/rmats.py"]
+
+sanity_check_commands = [
+    'rmats.py --version',
+]
+
+sanity_check_paths = {
+    'files': ['bin/rMATSexe', 'bin/rmats.py'],
+    'dirs': [],
+}
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/r/rMATS-turbo/rMATS-turbo-4.2.0_bamtools_as_dependency.patch b/easybuild/easyconfigs/r/rMATS-turbo/rMATS-turbo-4.2.0_bamtools_as_dependency.patch
@@ -0,0 +1,37 @@
+# author: Denis Kristak
+# this patch makes rMATS take bamtools from official dependencies, not from the downloaded folder
+# updated for new version by Samuel Moors (Vrije Universiteit Brussel)
+diff -ur rmats-turbo-4.2.0.orig/rMATS_pipeline/setup.py rmats-turbo-4.2.0/rMATS_pipeline/setup.py
+--- rmats-turbo-4.2.0.orig/rMATS_pipeline/setup.py	2023-10-18 18:33:06.000000000 +0200
++++ rmats-turbo-4.2.0/rMATS_pipeline/setup.py	2024-01-16 10:59:40.272152202 +0100
+@@ -5,15 +5,16 @@
+ from Cython.Build import cythonize
+ from Cython.Distutils import build_ext
+
+-bamtools_include = [os.path.abspath('../bamtools/include'),]
+-bamtools_lib = [os.path.abspath('../bamtools/lib'),]
++bamtools_root = os.environ['EBROOTBAMTOOLS']
++bamtools_include = bamtools_root + '/include/bamtools'
++bamtools_lib = bamtools_root + '/lib'
+ source_pattern = 'rmatspipeline/%s.pyx'
+
+ asevent_ext = [
+-    Extension('rmats.rmatspipeline', sources=[source_pattern % "rmatspipeline"],
+-              include_dirs=bamtools_include,
++    Extension('rmatspipeline', sources=[source_pattern % "rmatspipeline"],
++              include_dirs=[bamtools_include,],
+               libraries=['m','stdc++','bamtools','z'],
+-              library_dirs=bamtools_lib,
++              library_dirs=[bamtools_lib,],
+               extra_compile_args = ['-O3', '-funroll-loops',
+                                     '-std=c++11', '-fopenmp',
+                                     '-D__STDC_CONSTANT_MACROS',
+@@ -31,7 +32,7 @@
+     compiler_directives['legacy_implicit_noexcept'] = True
+
+ setup(
+-    name = 'rmats.rmatspipeline',
++    name = 'rmatspipeline',
+     ext_modules = cythonize(asevent_ext, compiler_directives=compiler_directives),
+     cmdclass = {'build_ext': build_ext},
+ )