diff --git a/236_NGSpeciesID/NGSpeciesID-0.3.0-foss-2022b.eb b/236_NGSpeciesID/NGSpeciesID-0.3.0-foss-2022b.eb
deleted file mode 100644
index 3206916b..00000000
--- a/236_NGSpeciesID/NGSpeciesID-0.3.0-foss-2022b.eb
+++ /dev/null
@@ -1,43 +0,0 @@
-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': '2022b'}
-
-sources = [SOURCE_TAR_GZ]
-checksums = ['71663ce280220d4e692cc6c3aea44f91e40b3143ed09a9462bdf2feb1d94aa9f']
-
-dependencies = [
-    ('Python', '3.10.8'),
-    ('python-parasail', '1.3.4'),
-    ('edlib', '1.3.9'),
-    # ('medaka', '1.6.0'),  # TODO only for 2022a
-    ('spoa', '4.0.7'),
-    ('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'
diff --git a/236_NGSpeciesID/NGSpeciesID-0.3.0-foss-2023a.eb b/236_NGSpeciesID/NGSpeciesID-0.3.0-foss-2023a.eb
index b9a14fc1..ad912110 100644
--- a/236_NGSpeciesID/NGSpeciesID-0.3.0-foss-2023a.eb
+++ b/236_NGSpeciesID/NGSpeciesID-0.3.0-foss-2023a.eb
@@ -14,7 +14,7 @@ checksums = ['71663ce280220d4e692cc6c3aea44f91e40b3143ed09a9462bdf2feb1d94aa9f']
 dependencies = [
     ('Python', '3.11.3'),
     ('python-parasail', '1.3.4'),
-    ('edlib', '1.2.7'),  # TODO change version to python-1.3.9
+    ('edlib', '1.3.9'),
     ('medaka', '1.11.3'),
     ('spoa', '4.1.0'),
     ('Racon', '1.5.0'),
diff --git a/236_NGSpeciesID/Racon-1.5.0-GCCcore-12.2.0.eb b/236_NGSpeciesID/Racon-1.5.0-GCCcore-12.2.0.eb
deleted file mode 100644
index 980263ed..00000000
--- a/236_NGSpeciesID/Racon-1.5.0-GCCcore-12.2.0.eb
+++ /dev/null
@@ -1,29 +0,0 @@
-easyblock = 'CMakeMake'
-
-name = 'Racon'
-version = '1.5.0'
-
-homepage = 'https://github.com/lbcb-sci/racon'
-description = """Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads."""
-
-toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
-
-github_account = 'lbcb-sci'
-source_urls = [GITHUB_SOURCE]
-sources = ['%(version)s.tar.gz']
-checksums = ['41e362f71cc03b934f17d6e2c0d626e1b2997258261b14551586de006666424a']
-
-builddependencies = [
-    ('CMake', '3.24.3'),
-    ('binutils', '2.39'),
-    ('git', '2.38.1', '-nodocs'),
-]
-
-sanity_check_paths = {
-    'files': ['bin/racon'],
-    'dirs': [],
-}
-
-sanity_check_commands = ['racon --help']
-
-moduleclass = 'bio'
diff --git a/236_NGSpeciesID/WhatsHap-2.1-foss-2022b.eb b/236_NGSpeciesID/WhatsHap-2.1-foss-2022b.eb
deleted file mode 100644
index d163bb3a..00000000
--- a/236_NGSpeciesID/WhatsHap-2.1-foss-2022b.eb
+++ /dev/null
@@ -1,50 +0,0 @@
-# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
-
-easyblock = 'PythonBundle'
-
-name = 'WhatsHap'
-version = '2.1'
-
-homepage = 'https://whatshap.readthedocs.io'
-description = """WhatsHap is a software for phasing genomic variants using DNA
-sequencing reads, also called read-based phasing or haplotype assembly. It is
-especially suitable for long reads, but works also well with short reads."""
-
-toolchain = {'name': 'foss', 'version': '2022b'}
-
-dependencies = [
-    ('Python', '3.10.8'),
-    ('Pysam', '0.21.0'),
-    ('networkx', '2.8.8'),
-    ('SciPy-bundle', '2023.02'),
-    ('Biopython', '1.81'),
-    ('Yasm', '1.3.0'),
-    ('pyfaidx', '0.7.2.1'),
-    ('python-isal', '1.1.0'),
-]
-
-sanity_pip_check = True
-use_pip = True
-
-exts_list = [
-    ('xopen', '1.7.0', {
-        'checksums': ['901f9c8298e95ed74767a4bd76d9f4cf71d8de27b8cf296ac3e7bc1c11520d9f'],
-    }),
-    ('pulp', '2.7.0', {
-        'source_tmpl': 'PuLP-%(version)s.tar.gz',
-        'checksums': ['e73ee6b32d639c9b8cf4b4aded334ba158be5f8313544e056f796ace0a10ae63'],
-    }),
-    (name, version, {
-        'source_tmpl': '%(namelower)s-%(version)s.tar.gz',
-        'checksums': ['9b61812eda1dd5251ba8d02db16d7ddda152ccc813cb3db6a1ec796f1865fe8d'],
-    }),
-]
-
-sanity_check_paths = {
-    'files': ['bin/%(namelower)s'],
-    'dirs': [],
-}
-
-sanity_check_commands = ['%(namelower)s --help']
-
-moduleclass = 'bio'
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
deleted file mode 100644
index 16c47468..00000000
--- a/236_NGSpeciesID/edlib-1.2.7-GCC-12.3.0.eb
+++ /dev/null
@@ -1,32 +0,0 @@
-easyblock = 'PythonBundle'
-
-name = 'edlib'
-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."
-
-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',
-        # TODO comment
-        'preinstallopts': 'cd bindings/python && make && python -m cogapp -d -o README.rst README-tmpl.rst && ',
-        'checksums': ['8767bc1b04a1a67282d57662e5702c4908996e96b1753b5520921ff189974621'],
-    }),
-]
-
-moduleclass = 'bio'
diff --git a/236_NGSpeciesID/edlib-1.3.9-GCC-12.3.0.eb.orig b/236_NGSpeciesID/edlib-1.3.9-GCC-12.3.0.eb.orig
deleted file mode 100644
index beab29cd..00000000
--- a/236_NGSpeciesID/edlib-1.3.9-GCC-12.3.0.eb.orig
+++ /dev/null
@@ -1,25 +0,0 @@
-easyblock = 'PythonPackage'
-
-name = 'edlib'
-version = '1.3.9'
-
-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'}
-
-sources = [SOURCE_TAR_GZ]
-checksums = ['64c3dfab3ebe3e759565a0cc71eb4df23cf3ce1713fd558af3c473dddc2a3766']
-
-dependencies = [
-    ('Python', '3.11.3'),
-    ('Python-bundle-PyPI', '2023.06'),
-]
-
-download_dep_fail = True
-use_pip = True
-sanity_pip_check = True
-
-moduleclass = 'bio'
-
-# TODO edlib.bycython.cpp:198:12: fatal error: longintrepr.h: No such file or directory
diff --git a/236_NGSpeciesID/intervaltree-python-3.1.0-GCCcore-12.2.0.eb b/236_NGSpeciesID/intervaltree-python-3.1.0-GCCcore-12.2.0.eb
deleted file mode 100644
index 40fb723e..00000000
--- a/236_NGSpeciesID/intervaltree-python-3.1.0-GCCcore-12.2.0.eb
+++ /dev/null
@@ -1,31 +0,0 @@
-# Author: Jasper Grimm (UoY)
-# Update: Petr Král (INUITS)
-
-easyblock = 'PythonPackage'
-
-name = 'intervaltree-python'
-_modname = 'intervaltree'
-version = '3.1.0'
-
-homepage = 'https://github.com/chaimleib/intervaltree'
-description = """A mutable, self-balancing interval tree. Queries may be by
- point, by range overlap, or by range containment.
-"""
-
-toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
-
-source_urls = ['https://pypi.python.org/packages/source/i/%s' % _modname]
-sources = ['%s-%s.tar.gz' % (_modname, version)]
-checksums = ['902b1b88936918f9b2a19e0e5eb7ccb430ae45cde4f39ea4b36932920d33952d']
-
-builddependencies = [('binutils', '2.39')]
-
-dependencies = [('Python', '3.10.8')]
-
-use_pip = True
-download_dep_fail = True
-sanity_pip_check = True
-
-options = {'modulename': _modname}
-
-moduleclass = 'bio'
diff --git a/236_NGSpeciesID/intervaltree-python-3.1.0-GCCcore-12.3.0.eb b/236_NGSpeciesID/intervaltree-python-3.1.0-GCCcore-12.3.0.eb
index 6e774dc9..4934ceb7 100644
--- a/236_NGSpeciesID/intervaltree-python-3.1.0-GCCcore-12.3.0.eb
+++ b/236_NGSpeciesID/intervaltree-python-3.1.0-GCCcore-12.3.0.eb
@@ -32,5 +32,3 @@ sanity_pip_check = True
 options = {'modulename': _modname}
 
 moduleclass = 'bio'
-
-# TODO intervaltree 3.1.0 requires sortedcontainers, which is not installed.
diff --git a/236_NGSpeciesID/medaka-1.11.1-foss-2022b.eb b/236_NGSpeciesID/medaka-1.11.1-foss-2022b.eb
deleted file mode 100644
index c1da588d..00000000
--- a/236_NGSpeciesID/medaka-1.11.1-foss-2022b.eb
+++ /dev/null
@@ -1,70 +0,0 @@
-# This is a contribution from HPCNow! (http://hpcnow.com)
-# Copyright::   HPCNow!
-# Authors::     Danilo Gonzalez <danilo.gonzalez@hpcnow.com>
-# License::     GPL-v3.0
-# Updated to foss-2020b to use with artic tool
-# J. Sassmannshausen (GSTT/NHS UK)
-# Updated to 1.5.0
-# Jasper Grimm (UoY)
-# Updated: Petr Král (INUITS)
-
-easyblock = 'PythonBundle'
-
-name = 'medaka'
-version = '1.11.1'
-
-homepage = 'https://github.com/nanoporetech/medaka'
-description = "medaka is a tool to create a consensus sequence from nanopore sequencing data."
-
-toolchain = {'name': 'foss', 'version': '2022b'}
-toolchainopts = {'pic': True}
-
-builddependencies = [('Autotools', '20220317')]
-
-_minimap_ver = '2.26'
-dependencies = [
-    ('Python', '3.10.8'),  # includes cffi
-    # tensorflow~=2.10.0 required by medaka 1.9.1, see requirements.txt
-    ('TensorFlow', '2.13.0'),
-    ('Pysam', '0.21.0'),
-    ('SAMtools', '1.17'),
-    ('minimap2', _minimap_ver),
-    ('HTSlib', '1.17'),  # for tabix, bgzip
-    ('Racon', '1.5.0'),
-    ('edlib', '1.3.9'),
-    # ('pyspoa', '0.2.1'),  # TODO
-    ('python-parasail', '1.3.4'),
-    ('ont-fast5-api', '4.1.1'),
-    ('WhatsHap', '2.1'),
-    ('intervaltree-python', '3.1.0'),
-    ('BCFtools', '1.17'),
-]
-
-use_pip = True
-sanity_pip_check = True
-
-exts_list = [
-    ('mappy', _minimap_ver, {
-        'checksums': ['e53fbe9a3ea8762a64b8103f4f779c9fb16d418eaa0a731f45cebc83867a9b71'],
-    }),
-    ('wurlitzer', '3.0.3', {
-        'checksums': ['224f5fe70618be3872c05dfddc8c457191ec1870654596279fcc1edadebe3e5b'],
-    }),
-    (name, version, {
-        'checksums': ['4440762a17ddd66806ddbd7c3218140caa234b96a8c919ed54d7243d3e4a5dd1'],
-        # Some requirements are too strict.
-        'preinstallopts': "sed -i 's/tensorflow.*/tensorflow/g;s/cffi==/cffi>=/g' requirements.txt && ",
-    }),
-]
-
-sanity_check_paths = {
-    'files': ['bin/medaka', 'bin/medaka_consensus', 'bin/medaka_version_report'],
-    'dirs': ['lib/python%(pyshortver)s/site-packages'],
-}
-
-sanity_check_commands = [
-    "medaka --help",
-    "medaka_version_report",
-]
-
-moduleclass = 'bio'
diff --git a/236_NGSpeciesID/medaka-1.11.3-foss-2023a.eb b/236_NGSpeciesID/medaka-1.11.3-foss-2023a.eb
index 7defdab4..989d24af 100644
--- a/236_NGSpeciesID/medaka-1.11.3-foss-2023a.eb
+++ b/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'),  # TODO change version to python-1.3.9
+    ('edlib', '1.3.9'),
     ('pyspoa', '0.2.1'),
     ('python-parasail', '1.3.4'),
     ('ont-fast5-api', '4.1.2'),
@@ -55,7 +55,7 @@ exts_list = [
         'checksums': ['940568212d152f573270967b02f6e841561cc43138b6aa15783c371457fef7b9'],
         # Some requirements are too strict.
         '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 && ",
+            + "sed -i 's/8, 9, 10/8, 9, 10, 11/g;s/,<3.11//g' setup.py && ",
     }),
 ]
 
diff --git a/236_NGSpeciesID/pyspoa-0.2.1-GCC-12.2.0.eb b/236_NGSpeciesID/pyspoa-0.2.1-GCC-12.2.0.eb
deleted file mode 100644
index 6fe09cd7..00000000
--- a/236_NGSpeciesID/pyspoa-0.2.1-GCC-12.2.0.eb
+++ /dev/null
@@ -1,64 +0,0 @@
-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'}
-
-toolchainopts = {'extra_cflags': "-fpermissive"}
-
-sources = [
-    {
-        'filename': '%(name)s-%(version)s.tar.gz',
-        'git_config': {
-            'url': 'https://github.com/nanoporetech',
-            'repo_name': 'pyspoa',
-            'tag': 'v%(version)s',
-            'recursive': True,
-            'keep_git_dir': True,
-        }
-    },
-    {
-        '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 = [
-    None,
-    '16a7ad9b31ba5880dac55d62b5d6f243c3ebc8d46a3514149e56b5e7ea81f85f',
-    '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 && "
-preinstallopts += "export libspoa=$EBROOTSPOA/lib/libspoa.a && "
-
-options = {'modulename': 'spoa'}
-
-sanity_check_commands = ["cd %(builddir)s/*/tests && python test_pyspoa.py"]
-
-moduleclass = 'lib'
-
-# TODO ERROR: `python test_pyspoa.py exited with code -11`