From 40597ae9a4fe0cf856dac2a9a177fe7844824f5e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Thu, 25 Jan 2024 17:26:15 +0100
Subject: [PATCH] progress on #236 NGSpeciesID

---
 236_NGSpeciesID/edlib-1.2.7-GCC-12.3.0.eb     | 33 +++++++++++++++++++
 ....3.0.eb => edlib-1.3.9-GCC-12.3.0.eb.orig} |  0
 236_NGSpeciesID/medaka-1.11.3-foss-2023a.eb   | 12 +++----
 3 files changed, 39 insertions(+), 6 deletions(-)
 create mode 100644 236_NGSpeciesID/edlib-1.2.7-GCC-12.3.0.eb
 rename 236_NGSpeciesID/{edlib-1.3.9-GCC-12.3.0.eb => edlib-1.3.9-GCC-12.3.0.eb.orig} (100%)

diff --git a/236_NGSpeciesID/edlib-1.2.7-GCC-12.3.0.eb b/236_NGSpeciesID/edlib-1.2.7-GCC-12.3.0.eb
new file mode 100644
index 00000000..8535acf8
--- /dev/null
+++ b/236_NGSpeciesID/edlib-1.2.7-GCC-12.3.0.eb
@@ -0,0 +1,33 @@
+easyblock = 'PythonBundle'
+
+name = 'edlib'
+version = '1.2.7'
+
+homepage = 'https://martinsos.github.io/edlib'
+description = "Lightweight, super fast library for sequence alignment using edit (Levenshtein) distance."
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('cogapp', '3.3.0', {
+        'checksums': ['1be95183f70282422d594fa42426be6923070a4bd8335621f6347f3aeee81db0'],
+    }),
+    (name, version, {
+        'source_urls': ['https://github.com/Martinsos/edlib/archive/'],
+        'source_tmpl': 'v%(version)s.tar.gz',
+        'preinstallopts': 'cd bindings/python && make && python -m cogapp -d -o README.rst README-tmpl.rst && ',
+        'checksums': ['8767bc1b04a1a67282d57662e5702c4908996e96b1753b5520921ff189974621'],
+    }),
+]
+
+moduleclass = 'bio'
+
+# TODO edlib.bycython.cpp:198:12: fatal error: longintrepr.h: No such file or directory
diff --git a/236_NGSpeciesID/edlib-1.3.9-GCC-12.3.0.eb b/236_NGSpeciesID/edlib-1.3.9-GCC-12.3.0.eb.orig
similarity index 100%
rename from 236_NGSpeciesID/edlib-1.3.9-GCC-12.3.0.eb
rename to 236_NGSpeciesID/edlib-1.3.9-GCC-12.3.0.eb.orig
diff --git a/236_NGSpeciesID/medaka-1.11.3-foss-2023a.eb b/236_NGSpeciesID/medaka-1.11.3-foss-2023a.eb
index 9b28a83e..86267451 100644
--- a/236_NGSpeciesID/medaka-1.11.3-foss-2023a.eb
+++ b/236_NGSpeciesID/medaka-1.11.3-foss-2023a.eb
@@ -27,17 +27,17 @@ dependencies = [
     ('Python-bundle-PyPI', '2023.06'),  # includes cffi
     # tensorflow~=2.10.0 required by medaka 1.9.1, see requirements.txt
     ('TensorFlow', '2.13.0'),
-    ('Pysam', '0.21.0'),
+    ('Pysam', '0.22.0'),
     ('SAMtools', '1.18'),
     ('minimap2', _minimap_ver),
     ('HTSlib', '1.18'),  # for tabix, bgzip
     ('Racon', '1.5.0'),
-    ('edlib', '1.3.9'),  # TODO
+    ('edlib', '1.2.7'),
     ('pyspoa', '0.2.1'),
     ('python-parasail', '1.3.4'),
-    ('ont-fast5-api', '4.1.1'),
-    ('WhatsHap', '2.1'),  # TODO
-    ('intervaltree-python', '3.1.0'),  # TODO
+    ('ont-fast5-api', '4.1.2'),
+    ('WhatsHap', '2.1'),
+    ('intervaltree-python', '3.1.0'),
     ('BCFtools', '1.18'),
 ]
 
@@ -52,7 +52,7 @@ exts_list = [
         'checksums': ['224f5fe70618be3872c05dfddc8c457191ec1870654596279fcc1edadebe3e5b'],
     }),
     (name, version, {
-        'checksums': ['4440762a17ddd66806ddbd7c3218140caa234b96a8c919ed54d7243d3e4a5dd1'],
+        'checksums': ['940568212d152f573270967b02f6e841561cc43138b6aa15783c371457fef7b9'],
         # Some requirements are too strict.
         'preinstallopts': "sed -i 's/tensorflow.*/tensorflow/g;s/cffi==/cffi>=/g' requirements.txt && ",
     }),