progress on #236 NGSpeciesID

236_NGSpeciesID/NGSpeciesID-0.3.0-foss-2023a.eb

@@ -0,0 +1,43 @@
+easyblock = 'PythonPackage'
+
+name = 'NGSpeciesID'
+version = '0.3.0'
+
+homepage = 'https://github.com/ksahlin/NGSpeciesID'
+description = "NGSpeciesID is a tool for clustering and consensus forming of targeted ONT reads."
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['71663ce280220d4e692cc6c3aea44f91e40b3143ed09a9462bdf2feb1d94aa9f']
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('python-parasail', '1.3.4'),
+    ('edlib', '1.2.7'),  # TODO change version to python-1.3.9
+    ('medaka', '1.11.3'),
+    ('spoa', '4.1.0'),
+    ('Racon', '1.5.0'),
+    ('minimap2', '2.26'),
+]
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+# no proper namespace for NGSpeciesID
+options = {'modulename': 'modules.consensus'}
+
+# parasail requirements are too strict
+preinstallopts = "sed -i 's/parasail==/parasail>=/g' setup.py && "
+
+sanity_check_paths = {
+    'files': ['bin/NGSpeciesID'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ["NGSpeciesID --help"]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'

236_NGSpeciesID/edlib-1.2.7-GCC-12.3.0.eb

@@ -1,7 +1,7 @@
 easyblock = 'PythonBundle'
 
 name = 'edlib'
-version = '1.2.7'
+version = '1.2.7'  # TODO change version to python-1.3.9
 
 homepage = 'https://martinsos.github.io/edlib'
 description = "Lightweight, super fast library for sequence alignment using edit (Levenshtein) distance."

236_NGSpeciesID/medaka-1.11.3-foss-2023a.eb

@@ -32,7 +32,7 @@ dependencies = [
     ('minimap2', _minimap_ver),
     ('HTSlib', '1.18'),  # for tabix, bgzip
     ('Racon', '1.5.0'),
-    ('edlib', '1.2.7'),
+    ('edlib', '1.2.7'),  # TODO change version to python-1.3.9
     ('pyspoa', '0.2.1'),
     ('python-parasail', '1.3.4'),
     ('ont-fast5-api', '4.1.2'),
@@ -54,7 +54,8 @@ exts_list = [
     (name, version, {
         'checksums': ['940568212d152f573270967b02f6e841561cc43138b6aa15783c371457fef7b9'],
         # Some requirements are too strict.
-        'preinstallopts': "sed -i 's/tensorflow.*/tensorflow/g;s/cffi==/cffi>=/g' requirements.txt && ",
+        'preinstallopts': "sed -i 's/tensorflow.*/tensorflow/g;s/cffi==/cffi>=/g' requirements.txt && "
+            + "sed -i 's/8, 9, 10/8, 9, 10, 11/g' setup.py && sed -i 's/,<3.11//g' setup.py && ",
     }),
 ]