progress on #236 NGSpeciesID

236_NGSpeciesID/NGSpeciesID-0.3.0-foss-2022b.eb

@@ -15,10 +15,10 @@ dependencies = [
     ('Python', '3.10.8'),
     ('python-parasail', '1.3.4'),
     ('edlib', '1.3.9'),
-    # ('medaka', '1.6.0'),  # needed? TODO only for 2022a
-    ('spoa', '4.0.7'),  # needed?
-    # ('Racon', '1.5.0'),  # needed? TODO only for 2022a
-    ('minimap2', '2.26'),  # needed?
+    # ('medaka', '1.6.0'),  # TODO only for 2022a
+    ('spoa', '4.0.7'),
+    ('Racon', '1.5.0'),
+    ('minimap2', '2.26'),
 ]
 
 download_dep_fail = True

236_NGSpeciesID/medaka-1.11.1-foss-2022b.eb

@@ -32,7 +32,7 @@ dependencies = [
     ('HTSlib', '1.17'),  # for tabix, bgzip
     ('Racon', '1.5.0'),
     ('edlib', '1.3.9'),
-    ('pyspoa', '0.0.9'),
+    # ('pyspoa', '0.2.1'),  # TODO
     ('python-parasail', '1.3.4'),
     ('ont-fast5-api', '4.1.1'),
     ('WhatsHap', '2.1'),
@@ -41,24 +41,22 @@ dependencies = [
 ]
 
 use_pip = True
+sanity_pip_check = True
 
 exts_list = [
     ('mappy', _minimap_ver, {
         'checksums': ['e53fbe9a3ea8762a64b8103f4f779c9fb16d418eaa0a731f45cebc83867a9b71'],
     }),
+    ('wurlitzer', '3.0.3', {
+        'checksums': ['224f5fe70618be3872c05dfddc8c457191ec1870654596279fcc1edadebe3e5b'],
+    }),
     (name, version, {
         'checksums': ['4440762a17ddd66806ddbd7c3218140caa234b96a8c919ed54d7243d3e4a5dd1'],
-        # remove TensorFlow version requirement which is too strict
-        'preinstallopts': "sed -i 's/tensorflow.*/tensorflow/g' requirements.txt && ",
+        # Some requirements are too strict.
+        'preinstallopts': "sed -i 's/tensorflow.*/tensorflow/g;s/cffi==/cffi>=/g' requirements.txt && ",
     }),
 ]
 
-# TODO medaka 1.11.1 requires wurlitzer, which is not installed.
-#      medaka 1.11.1 has requirement cffi==1.15.0, but you have cffi 1.15.1.
-#      medaka 1.11.1 has requirement pyspoa>=0.2.1, but you have pyspoa 0.0
-
-sanity_pip_check = True
-
 sanity_check_paths = {
     'files': ['bin/medaka', 'bin/medaka_consensus', 'bin/medaka_version_report'],
     'dirs': ['lib/python%(pyshortver)s/site-packages'],

236_NGSpeciesID/pyspoa-0.2.1-GCC-12.2.0.eb

@@ -0,0 +1,40 @@
+easyblock = 'PythonPackage'
+
+name = 'pyspoa'
+version = '0.2.1'
+
+local_cereal_version = '1.3.2'
+
+homepage = 'https://github.com/nanoporetech/pyspoa'
+description = "Python bindings to spoa."
+
+toolchain = {'name': 'GCC', 'version': '12.2.0'}
+
+sources = [SOURCE_TAR_GZ]
+patches = ['pyspoa-%(version)s_use-spoa-dep.patch']
+checksums = [
+    {'pyspoa-0.2.1.tar.gz': 'dad5f244dc524a2fd49d4b4918ce58d31db351fca34696b1d5f391aa66de7645'},
+    {'pyspoa-0.2.1_use-spoa-dep.patch': 'dffd946e3b36e4872846fe983d287f992b5bf177798e11141bf0d645cfc0664d'},
+]
+
+builddependencies = [('CMake', '3.24.3')]
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('pybind11', '2.10.3'),
+    ('spoa', '4.0.7'),
+]
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+preinstallopts = "mkdir -p src/vendor/cereal && ln -s %(builddir)s/cereal-*/include src/vendor/cereal/include && "
+# strip out cmake requirements, since we provide that as proper dependency
+preinstallopts += "sed -i 's/.cmake==[0-9.]*.//g' setup.py && "
+
+options = {'modulename': 'spoa'}
+
+sanity_check_commands = ["cd %(builddir)s/*/tests && python test_pyspoa.py"]
+
+moduleclass = 'lib'

236_NGSpeciesID/pyspoa-0.2.1-GCC-12.2.0.eb.backup

@@ -0,0 +1,53 @@
+easyblock = 'PythonPackage'
+
+name = 'pyspoa'
+version = '0.2.1'
+
+local_cereal_version = '1.3.2'
+
+homepage = 'https://github.com/nanoporetech/pyspoa'
+description = "Python bindings to spoa."
+
+toolchain = {'name': 'GCC', 'version': '12.2.0'}
+
+sources = [
+    {
+        'source_urls': ['https://github.com/nanoporetech/pyspoa/archive/'],
+        'download_filename': 'v%(version)s.tar.gz',
+        'filename': 'pyspoa-%(version)s.tar.gz',
+    },
+    {
+        'source_urls': ['https://github.com/USCiLab/cereal/archive/'],
+        'download_filename': 'v%s.tar.gz' % local_cereal_version,
+        'filename': 'cereal-%s.tar.gz' % local_cereal_version,
+    },
+]
+patches = ['pyspoa-%(version)s_use-spoa-dep.patch']
+
+checksums = [
+    {'pyspoa-%s.tar.gz' % version: 'dad5f244dc524a2fd49d4b4918ce58d31db351fca34696b1d5f391aa66de7645'},
+    {'cereal-%s.tar.gz' % local_cereal_version: '16a7ad9b31ba5880dac55d62b5d6f243c3ebc8d46a3514149e56b5e7ea81f85f'},
+    {'pyspoa-%s_use-spoa-dep.patch' % version: 'dffd946e3b36e4872846fe983d287f992b5bf177798e11141bf0d645cfc0664d'},
+]
+
+builddependencies = [('CMake', '3.24.3')]
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('pybind11', '2.10.3'),
+    ('spoa', '4.0.7'),
+]
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+preinstallopts = "mkdir -p src/vendor/cereal && ln -s %(builddir)s/cereal-*/include src/vendor/cereal/include && "
+# strip out cmake requirements, since we provide that as proper dependency
+preinstallopts += "sed -i 's/.cmake==[0-9.]*.//g' setup.py && "
+
+options = {'modulename': 'spoa'}
+
+sanity_check_commands = ["cd %(builddir)s/*/tests && python test_pyspoa.py"]
+
+moduleclass = 'lib'

236_NGSpeciesID/pyspoa-0.2.1_use-spoa-dep.patch

@@ -0,0 +1,24 @@
+use spoa dependency provided through EasyBuild
+
+author: Kenneth Hoste (HPC-UGent)
+updated by: Petr Král (Inuits)
+diff --git a/pyspoa-0.2.1/setup.py.orig b/pyspoa-0.2.1/setup.py
+--- a/pyspoa-0.2.1/setup.py.orig	2023-11-27 14:48:14.661356275 +0100
++++ b/pyspoa-0.2.1/setup.py	2023-11-27 14:52:53.880656275 +0100
+@@ -119,14 +119,14 @@
+         'spoa',
+         ['pyspoa.cpp'],
+         include_dirs=[
+-            'src/include/spoa',
++            os.path.join(os.getenv('EBROOTSPOA'), 'include/spoa'),
+             'src/vendor/cereal/include',
+             get_pybind_include(),
+             get_pybind_include(user=True),
+         ],
+         language='c++',
+         extra_objects=[
+-            LIB_SPOA
++            os.path.join(os.getenv('EBROOTSPOA'), 'lib64/libspoa.a'),
+         ],
+
+     ),