From 713c6e0a0d91ac6fbca62d1eec135cd1b670d3bb Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Wed, 17 Jul 2024 17:50:07 +0200
Subject: [PATCH] #235 smafa + cd-hit + polars

---
 235_singleM/SingleM-0.16.0-foss-2023a.eb      |  84 +-
 235_singleM/cdhit.eb                          |  39 +
 235_singleM/crates_smafa.txt                  | 105 ++
 .../ExpressBetaDiversity-1.0.10-GCC-12.3.0.eb |   0
 .../Seqmagick-0.8.6-foss-2023a.eb             |   0
 235_singleM/polars.eb                         | 908 ++++++++++++++++++
 235_singleM/smafa.eb                          | 235 +++++
 357_Synthcity/synthcity.eb                    |   1 +
 8 files changed, 1350 insertions(+), 22 deletions(-)
 create mode 100644 235_singleM/cdhit.eb
 create mode 100644 235_singleM/crates_smafa.txt
 rename 235_singleM/{ => merged}/ExpressBetaDiversity-1.0.10-GCC-12.3.0.eb (100%)
 rename 235_singleM/{ => merged}/Seqmagick-0.8.6-foss-2023a.eb (100%)
 create mode 100644 235_singleM/polars.eb
 create mode 100644 235_singleM/smafa.eb

diff --git a/235_singleM/SingleM-0.16.0-foss-2023a.eb b/235_singleM/SingleM-0.16.0-foss-2023a.eb
index 91b22d88..45bdfc2b 100644
--- a/235_singleM/SingleM-0.16.0-foss-2023a.eb
+++ b/235_singleM/SingleM-0.16.0-foss-2023a.eb
@@ -11,29 +11,72 @@ finding bias in genome recovery, computing ecological diversity metrics, and lin
 
 toolchain = {'name': 'foss', 'version': '2023a'}
 
+# DEPS
+    # OK - python>=3.7 #, <3.10 # https://github.com/google-research/google-research/issues/779 means scann (at least 1.2.8) fails to install via pip for 3.10. Older python versions than 3.7 may also work, not tested.
+    # OK - diamond>=2.1.7 # Getting segmentation fault on test_insert_prefilter otherwise
+    # OK - biopython
+    # OK - hmmer
+    # OK - orfm
+    # OK - mfqe
+    # ok - extern
+    # ok - graftm>=0.15.0 # Version needed for --translation-table
+    # OK - krona
+    # OK - pplacer
+    # OK - sra-tools
+    # OK - ncbi-ngs-sdk - in SRA-Toolkit
+    # OK - sqlite - in python
+    # ok - squarify
+    # OK - mafft
+    # OK - seqmagick
+    # OK - expressbetadiversity
+    # OK - cd-hit -> created
+    # OK - fasttree
+    # ok - fastalite
+    # OK - jinja2 - pypi bundle
+    # OK - pip
+    # OK - sqlalchemy
+    # OK - pandas
+    # ok - bird_tool_utils_python>=0.4.1
+    # ok - zenodo_backpack
+    # OK - smafa>=0.7.0 -> created
+    # ok - pyranges
+    # OK - polars>=0.19.3 # supplement with taxon genome length requires this, for strip_chars
+    # OK - prodigal
+    # OK - tqdm
+    # OK - pyarrow
+    # # - galah >= 0.4.0 # 0.4.0 is the first version with checkm2 quality inputs, but not yet released 
+    # - pytest # For testing only
+    # - ipython # For testing only
+    # - sqlparse # Don't understand why, but this isn't being installed before tests are run on GH actions. Required indirectly (by taxtastic).
+    
 dependencies = [
     ('Python', '3.11.3'), # with SQLite
+    ('Python-bundle-PyPI', '2023.06'),
     ('SciPy-bundle', '2023.07'),  # for pandas
-    ('matplotlib', '3.7.2'),
+    # ('matplotlib', '3.7.2'),
     ('Biopython', '1.83'), 
-    ('polars', '0.19.19'), # polars >= 0.19.3 
+    ('polars', '0.20.2'), # polars >= 0.19.3 
     ('tqdm', '4.66.1'),
     ('Arrow', '14.0.1'), # for pyarrow
     ('DIAMOND', '2.1.8'),
     ('HMMER', '3.4'),
     ('MAFFT', '7.520', '-with-extensions'),
-    ('tqdm', '4.66.1'),
     ('OrfM', '0.7.1'),
     ('mfqe', '0.5.0'),
     ('KronaTools', '2.8.1'),
-    ('pplacer', '1.1.alpha19', '', True),
+    ('pplacer', '1.1.alpha19', '', SYSTEM),
     ('SRA-Toolkit', '3.0.10'),
     ('Seqmagick', '0.8.6'),
     ('ExpressBetaDiversity', '1.0.10'),
+    ('FastTree', '2.1.11'),
+    ('SQLAlchemy', '2.0.25'),
+    ('CD-HIT', '4.8.1'),
+    ('smafa', '0.8.0'),
+    ('prodigal', '2.6.3'),
+    #
     # ('DendroPy', '4.4.0'),
     # ('PyYAML', '5.1'),
     # ('PostgreSQL', '11.3', versionsuffix),  # required for psycopg2
-    # ('smafa', '0.4.0'),
     # ('VSEARCH', '2.13.4'),
     # ('fxtract', '2.3'),
 ]
@@ -41,30 +84,27 @@ dependencies = [
 use_pip = True
 sanity_pip_check = True
 
-# required because we're building Python packages using Intel compilers on top of Python built with GCC
-# check_ldshared = True
-
- # ('zenodo_backpack', '0.2.0', {
-#     'checksums': ['5843a04b353ae613b474932c2a12d1fbfd529674074e73927ddc131eba7f1da8'],
-# }),
-
-# ('bird_tool_utils', '0.4.1', {
-#     'checksums': ['6fe80f9608626427e8d382c5341c24088d61f17336fb6ce834d40aa4577499b5'],
-# }),
 exts_list = [
-    ('Jinja2', '3.1.3'),
-    ('fastalite', '0.4.1'),
+    ('zenodo_backpack', '0.3.1', {
+        'checksums': ['dc91f3c427f976465789746e94736abfa536cf42dc2e49b6d6067382a9a39b26'],
+    }),
+    ('bird_tool_utils', '0.4.1', {
+        'checksums': ['6fe80f9608626427e8d382c5341c24088d61f17336fb6ce834d40aa4577499b5'],
+    }),
+    ('fastalite', '0.4.1', {
+        'checksums': ['e85413ee22bdb3fe0f73f5226771cf71eb33074ccdf8bbefff3a1bc6242de37c'],
+    }),
+    ('squarify', '0.4.3', {
+        'checksums': ['54091f6ad175f7f201f8934574e647ce1b50dedc478c5fd968688eb7d7469f95'],
+    }),
     ('pyranges', '0.0.129', {
         'checksums': ['bee83b4fad0062be9586668c6b0fc4270d5e761951975e018202993680071fb3'],
     }),
-    ('SQLAlchemy', '2.0.25', {
-        'checksums': ['a2c69a7664fb2d54b8682dd774c3b54f67f84fa123cf84dda2a5f40dcaa04e08'],
-    }),
     ('extern', '0.4.1', {
         'checksums': ['0ff01adc2ad423f3d1e31641024b3974569fb0127b4d925bc6bed1cb86b6b1e4'],
     }),
-    ('graftm', '0.15.0', {
-        'checksums': ['794b2c6a8fff36c81db8b9a544ac021ab1397c569638bf7651ce5329db36de21'],
+    ('graftm', '0.15.1', {
+        'checksums': ['80d828c311d2d6067977cfad5b6bac7cbc5d223ef8ab770d676b39bf2bc75163'],
     }),
     ('singlem', version, {
         'checksums': ['64e43a6a40795d68ff5aed7dfff9a94532b862f25a28c27de7d588d64a8c7f79'],
diff --git a/235_singleM/cdhit.eb b/235_singleM/cdhit.eb
new file mode 100644
index 00000000..e07a87aa
--- /dev/null
+++ b/235_singleM/cdhit.eb
@@ -0,0 +1,39 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# changed toolchain and Perl version
+# Updated by: Thomas Eylenbosch(Gluo N.V.), Pavel Tománek (Inuits)
+
+easyblock = 'MakeCp'
+
+name = 'CD-HIT'
+version = '4.8.1'
+
+homepage = 'http://weizhongli-lab.org/cd-hit/'
+description = """ CD-HIT is a very widely used program for clustering and 
+ comparing protein or nucleotide sequences."""
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+toolchainopts = {'openmp': True}
+
+source_urls = ['https://github.com/weizhongli/cdhit/releases/download/V%(version)s/']
+sources = ['%(namelower)s-v%(version)s-2019-0228.tar.gz']
+checksums = ['26172dba3040d1ae5c73ff0ac6c3be8c8e60cc49fc7379e434cdf9cb1e7415de']
+
+dependencies = [
+    ('Perl', '5.36.1'),
+    ('zlib', '1.2.13'),
+]
+
+buildopts = ' CC="$CXX" CCFLAGS="$CPPFLAGS $CXXFLAGS"'
+
+local_list_of_executables = ['cd-hit', 'cd-hit-est', 'cd-hit-2d', 'cd-hit-est-2d', 'cd-hit-div', 'cd-hit-454']
+
+files_to_copy = [(local_list_of_executables, 'bin'), (['*.pl'], 'bin'), 'README', 'doc', 'license.txt']
+
+fix_perl_shebang_for = ['bin/*.pl']
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in local_list_of_executables],
+    'dirs': [],
+}
+
+moduleclass = 'bio'
diff --git a/235_singleM/crates_smafa.txt b/235_singleM/crates_smafa.txt
new file mode 100644
index 00000000..8deba62d
--- /dev/null
+++ b/235_singleM/crates_smafa.txt
@@ -0,0 +1,105 @@
+[('smafa', '0.8.0')]
+crates = [
+    ('addr2line', '0.22.0'),
+    ('adler', '1.0.2'),
+    ('aho-corasick', '1.1.3'),
+    ('anstream', '0.6.14'),
+    ('anstyle', '1.0.7'),
+    ('anstyle-parse', '0.2.4'),
+    ('anstyle-query', '1.1.0'),
+    ('anstyle-wincon', '3.0.3'),
+    ('assert_cli', '0.6.3'),
+    ('atomic-polyfill', '1.0.3'),
+    ('autocfg', '1.3.0'),
+    ('backtrace', '0.3.73'),
+    ('bird_tool_utils', '0.4.1'),
+    ('bird_tool_utils-man', '0.4.0'),
+    ('bitflags', '2.6.0'),
+    ('buffer-redux', '1.0.1'),
+    ('bytecount', '0.6.8'),
+    ('byteorder', '1.5.0'),
+    ('bzip2', '0.4.4'),
+    ('bzip2-sys', '0.1.11+1.0.8'),
+    ('cargo-husky', '1.5.0'),
+    ('cc', '1.1.5'),
+    ('cfg-if', '1.0.0'),
+    ('clap', '4.5.9'),
+    ('clap_builder', '4.5.9'),
+    ('clap_lex', '0.7.1'),
+    ('cobs', '0.2.3'),
+    ('colorchoice', '1.0.1'),
+    ('colored', '1.9.4'),
+    ('crc32fast', '1.4.2'),
+    ('critical-section', '1.1.2'),
+    ('difference', '2.0.0'),
+    ('embedded-io', '0.4.0'),
+    ('env_logger', '0.10.2'),
+    ('environment', '0.1.1'),
+    ('errno', '0.3.9'),
+    ('failure', '0.1.8'),
+    ('failure_derive', '0.1.8'),
+    ('fastrand', '2.1.0'),
+    ('flate2', '1.0.30'),
+    ('gimli', '0.29.0'),
+    ('hash32', '0.2.1'),
+    ('heapless', '0.7.17'),
+    ('hermit-abi', '0.3.9'),
+    ('humantime', '2.1.0'),
+    ('is-terminal', '0.4.12'),
+    ('is_terminal_polyfill', '1.70.0'),
+    ('itoa', '1.0.11'),
+    ('lazy_static', '1.5.0'),
+    ('libc', '0.2.155'),
+    ('linux-raw-sys', '0.4.14'),
+    ('lock_api', '0.4.12'),
+    ('log', '0.4.22'),
+    ('lzma-sys', '0.1.20'),
+    ('memchr', '2.7.4'),
+    ('miniz_oxide', '0.7.4'),
+    ('needletail', '0.5.1'),
+    ('object', '0.36.1'),
+    ('pkg-config', '0.3.30'),
+    ('postcard', '1.0.8'),
+    ('proc-macro2', '1.0.86'),
+    ('quote', '1.0.36'),
+    ('regex', '1.10.5'),
+    ('regex-automata', '0.4.7'),
+    ('regex-syntax', '0.8.4'),
+    ('roff', '0.1.0'),
+    ('rustc-demangle', '0.1.24'),
+    ('rustc_version', '0.4.0'),
+    ('rustix', '0.38.34'),
+    ('ryu', '1.0.18'),
+    ('scopeguard', '1.2.0'),
+    ('semver', '1.0.23'),
+    ('serde', '1.0.204'),
+    ('serde_derive', '1.0.204'),
+    ('serde_json', '1.0.120'),
+    ('spin', '0.9.8'),
+    ('stable_deref_trait', '1.2.0'),
+    ('strsim', '0.11.1'),
+    ('syn', '1.0.109'),
+    ('syn', '2.0.71'),
+    ('synstructure', '0.12.6'),
+    ('tempfile', '3.10.1'),
+    ('termcolor', '1.4.1'),
+    ('unicode-ident', '1.0.12'),
+    ('unicode-xid', '0.2.4'),
+    ('utf8parse', '0.2.2'),
+    ('version-compare', '0.1.1'),
+    ('winapi', '0.3.9'),
+    ('winapi-i686-pc-windows-gnu', '0.4.0'),
+    ('winapi-util', '0.1.8'),
+    ('winapi-x86_64-pc-windows-gnu', '0.4.0'),
+    ('windows-sys', '0.52.0'),
+    ('windows-targets', '0.52.6'),
+    ('windows_aarch64_gnullvm', '0.52.6'),
+    ('windows_aarch64_msvc', '0.52.6'),
+    ('windows_i686_gnu', '0.52.6'),
+    ('windows_i686_gnullvm', '0.52.6'),
+    ('windows_i686_msvc', '0.52.6'),
+    ('windows_x86_64_gnu', '0.52.6'),
+    ('windows_x86_64_gnullvm', '0.52.6'),
+    ('windows_x86_64_msvc', '0.52.6'),
+    ('xz2', '0.1.7'),
+]
diff --git a/235_singleM/ExpressBetaDiversity-1.0.10-GCC-12.3.0.eb b/235_singleM/merged/ExpressBetaDiversity-1.0.10-GCC-12.3.0.eb
similarity index 100%
rename from 235_singleM/ExpressBetaDiversity-1.0.10-GCC-12.3.0.eb
rename to 235_singleM/merged/ExpressBetaDiversity-1.0.10-GCC-12.3.0.eb
diff --git a/235_singleM/Seqmagick-0.8.6-foss-2023a.eb b/235_singleM/merged/Seqmagick-0.8.6-foss-2023a.eb
similarity index 100%
rename from 235_singleM/Seqmagick-0.8.6-foss-2023a.eb
rename to 235_singleM/merged/Seqmagick-0.8.6-foss-2023a.eb
diff --git a/235_singleM/polars.eb b/235_singleM/polars.eb
new file mode 100644
index 00000000..69b33e97
--- /dev/null
+++ b/235_singleM/polars.eb
@@ -0,0 +1,908 @@
+easyblock = 'CargoPythonPackage'
+
+name = 'polars'
+version = '0.20.2'
+
+homepage = 'https://pola.rs/'
+description = """Polars is a blazingly fast DataFrame library for manipulating
+structured data. The core is written in Rust and this module provides its
+interface for Python."""
+
+toolchain = {'name': 'gfbf', 'version': '2023a'}
+
+sources = [SOURCELOWER_TAR_GZ]
+checksums = [
+    {'polars-0.20.2.tar.gz': '483562f157e6aef6cb4343bf13d11295c8bff55ee62fef8010975a5fc22ff4e0'},
+    {'addr2line-0.21.0.tar.gz': '8a30b2e23b9e17a9f90641c7ab1549cd9b44f296d3ccbf309d2863cfe398a0cb'},
+    {'adler-1.0.2.tar.gz': 'f26201604c87b1e01bd3d98f8d5d9a8fcbb815e8cedb41ffccbeb4bf593a35fe'},
+    {'adler32-1.2.0.tar.gz': 'aae1277d39aeec15cb388266ecc24b11c80469deae6067e17a1a7aa9e5c1f234'},
+    {'ahash-0.8.6.tar.gz': '91429305e9f0a25f6205c5b8e0d2db09e0708a7a6df0f42212bb56c32c8ac97a'},
+    {'aho-corasick-1.1.2.tar.gz': 'b2969dcb958b36655471fc61f7e416fa76033bdd4bfed0678d8fee1e2d07a1f0'},
+    {'alloc-no-stdlib-2.0.4.tar.gz': 'cc7bb162ec39d46ab1ca8c77bf72e890535becd1751bb45f64c597edb4c8c6b3'},
+    {'alloc-stdlib-0.2.2.tar.gz': '94fb8275041c72129eb51b7d0322c29b8387a0386127718b096429201a5d6ece'},
+    {'allocator-api2-0.2.16.tar.gz': '0942ffc6dcaadf03badf6e6a2d0228460359d5e34b57ccdc720b7382dfbd5ec5'},
+    {'android-tzdata-0.1.1.tar.gz': 'e999941b234f3131b00bc13c22d06e8c5ff726d1b6318ac7eb276997bbb4fef0'},
+    {'android_system_properties-0.1.5.tar.gz': '819e7219dbd41043ac279b19830f2efc897156490d7fd6ea916720117ee66311'},
+    {'anes-0.1.6.tar.gz': '4b46cbb362ab8752921c97e041f5e366ee6297bd428a31275b9fcf1e380f7299'},
+    {'anstyle-1.0.4.tar.gz': '7079075b41f533b8c61d2a4d073c4676e1f8b249ff94a393b0595db304e0dd87'},
+    {'anyhow-1.0.75.tar.gz': 'a4668cab20f66d8d020e1fbc0ebe47217433c1b6c8f2040faf858554e394ace6'},
+    {'apache-avro-0.16.0.tar.gz': 'ceb7c683b2f8f40970b70e39ff8be514c95b96fcb9c4af87e1ed2cb2e10801a0'},
+    {'argminmax-0.6.1.tar.gz': '202108b46429b765ef483f8a24d5c46f48c14acfdacc086dd4ab6dddf6bcdbd2'},
+    {'array-init-cursor-0.2.0.tar.gz': 'bf7d0a018de4f6aa429b9d33d69edf69072b1c5b1cb8d3e4a5f7ef898fc3eb76'},
+    {'arrow-array-49.0.0.tar.gz': '6bda9acea48b25123c08340f3a8ac361aa0f74469bb36f5ee9acf923fce23e9d'},
+    {'arrow-buffer-49.0.0.tar.gz': '01a0fc21915b00fc6c2667b069c1b64bdd920982f426079bc4a7cab86822886c'},
+    {'arrow-data-49.0.0.tar.gz': '907fafe280a3874474678c1858b9ca4cb7fd83fb8034ff5b6d6376205a08c634'},
+    {'arrow-format-0.8.1.tar.gz': '07884ea216994cdc32a2d5f8274a8bee979cfe90274b83f86f440866ee3132c7'},
+    {'arrow-schema-49.0.0.tar.gz': '09e28a5e781bf1b0f981333684ad13f5901f4cd2f20589eab7cf1797da8fc167'},
+    {'arrow2-0.17.4.tar.gz': '59c468daea140b747d781a1da9f7db5f0a8e6636d4af20cc539e43d05b0604fa'},
+    {'async-stream-0.3.5.tar.gz': 'cd56dd203fef61ac097dd65721a419ddccb106b2d2b70ba60a6b529f03961a51'},
+    {'async-stream-impl-0.3.5.tar.gz': '16e62a023e7c117e27523144c5d2459f4397fcc3cab0085af8e2224f643a0193'},
+    {'async-trait-0.1.74.tar.gz': 'a66537f1bb974b254c98ed142ff995236e81b9d0fe4db0575f46612cb15eb0f9'},
+    {'atoi-2.0.0.tar.gz': 'f28d99ec8bfea296261ca1af174f24225171fea9664ba9003cbebee704810528'},
+    {'atoi_simd-0.15.5.tar.gz': 'ccfc14f5c3e34de57539a7ba9c18ecde3d9bbde48d232ea1da3e468adb307fd0'},
+    {'autocfg-1.1.0.tar.gz': 'd468802bab17cbc0cc575e9b053f41e72aa36bfa6b7f55e3529ffa43161b97fa'},
+    {'avro-schema-0.3.0.tar.gz': 'b5281855b39aba9684d2f47bf96983fbfd8f1725f12fabb0513a8ab879647bbd'},
+    {'aws-config-1.0.3.tar.gz': '004dc45f6b869e6a70725df448004a720b7f52f6607d55d8815cbd5448f86def'},
+    {'aws-credential-types-1.0.3.tar.gz': 'cfa51c87f10211f37cd78e6d01d6f18b3f96a086906ed361d11e04ac53e29508'},
+    {'aws-http-0.60.0.tar.gz': '361c4310fdce94328cc2d1ca0c8a48c13f43009c61d3367585685a50ca8c66b6'},
+    {'aws-runtime-1.0.3.tar.gz': 'ce0953f7fc1c4428511345e28ea3e98c8b59c9e91eafae30bf76d71d70642693'},
+    {'aws-sdk-s3-1.7.0.tar.gz': 'c1c12ff4dee4cbcfb0f7b7c19b1f72d5603ff8cd1183db7678a10ecf378ba534'},
+    {'aws-sdk-sso-1.6.0.tar.gz': '86575c7604dcdb583aba3390200e5333d8e4fe597bad54f57b190aaf4fac9771'},
+    {'aws-sdk-ssooidc-1.6.0.tar.gz': 'bef0d7c1d0730adb5e85407174483a579e39576e0f4350ecd0fac69ec1217b1b'},
+    {'aws-sdk-sts-1.6.0.tar.gz': 'f45778089751d5aa8645a02dd60865fa0eea39f00be5db2c7779bc50b83db19a'},
+    {'aws-sigv4-1.0.3.tar.gz': 'b6bcbad6e0f130232b22e4b4e28834348ce5b79c23b5059b387c08fd0dc8f876'},
+    {'aws-smithy-async-1.1.1.tar.gz': '1e9f65000917e3aa94c259d67fe01fa9e4cd456187d026067d642436e6311a81'},
+    {'aws-smithy-checksums-0.60.1.tar.gz': '4c2a63681f82fb85ca58d566534b7dc619c782fee0c61c1aa51e2b560c21cb4f'},
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+    {'xmlparser-0.13.6.tar.gz': '66fee0b777b0f5ac1c69bb06d361268faafa61cd4682ae064a171c16c433e9e4'},
+    {'xxhash-rust-0.8.7.tar.gz': '9828b178da53440fa9c766a3d2f73f7cf5d0ac1fe3980c1e5018d899fd19e07b'},
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+    {'zeroize-1.7.0.tar.gz': '525b4ec142c6b68a2d10f01f7bbf6755599ca3f81ea53b8431b7dd348f5fdb2d'},
+    {'zstd-0.13.0.tar.gz': 'bffb3309596d527cfcba7dfc6ed6052f1d39dfbd7c867aa2e865e4a449c10110'},
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+]
+
+crates = [
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+    ('adler', '1.0.2'),
+    ('adler32', '1.2.0'),
+    ('ahash', '0.8.6'),
+    ('aho-corasick', '1.1.2'),
+    ('alloc-no-stdlib', '2.0.4'),
+    ('alloc-stdlib', '0.2.2'),
+    ('allocator-api2', '0.2.16'),
+    ('android-tzdata', '0.1.1'),
+    ('android_system_properties', '0.1.5'),
+    ('anes', '0.1.6'),
+    ('anstyle', '1.0.4'),
+    ('anyhow', '1.0.75'),
+    ('apache-avro', '0.16.0'),
+    ('argminmax', '0.6.1'),
+    ('array-init-cursor', '0.2.0'),
+    ('arrow-array', '49.0.0'),
+    ('arrow-buffer', '49.0.0'),
+    ('arrow-data', '49.0.0'),
+    ('arrow-format', '0.8.1'),
+    ('arrow-schema', '49.0.0'),
+    ('arrow2', '0.17.4'),
+    ('async-stream', '0.3.5'),
+    ('async-stream-impl', '0.3.5'),
+    ('async-trait', '0.1.74'),
+    ('atoi', '2.0.0'),
+    ('atoi_simd', '0.15.5'),
+    ('autocfg', '1.1.0'),
+    ('avro-schema', '0.3.0'),
+    ('aws-config', '1.0.3'),
+    ('aws-credential-types', '1.0.3'),
+    ('aws-http', '0.60.0'),
+    ('aws-runtime', '1.0.3'),
+    ('aws-sdk-s3', '1.7.0'),
+    ('aws-sdk-sso', '1.6.0'),
+    ('aws-sdk-ssooidc', '1.6.0'),
+    ('aws-sdk-sts', '1.6.0'),
+    ('aws-sigv4', '1.0.3'),
+    ('aws-smithy-async', '1.1.1'),
+    ('aws-smithy-checksums', '0.60.1'),
+    ('aws-smithy-eventstream', '0.60.1'),
+    ('aws-smithy-http', '0.60.1'),
+    ('aws-smithy-json', '0.60.1'),
+    ('aws-smithy-query', '0.60.1'),
+    ('aws-smithy-runtime', '1.1.1'),
+    ('aws-smithy-runtime-api', '1.1.1'),
+    ('aws-smithy-types', '1.1.1'),
+    ('aws-smithy-xml', '0.60.1'),
+    ('aws-types', '1.0.3'),
+    ('backtrace', '0.3.69'),
+    ('base16ct', '0.1.1'),
+    ('base64', '0.21.5'),
+    ('base64-simd', '0.8.0'),
+    ('base64ct', '1.6.0'),
+    ('bincode', '1.3.3'),
+    ('bitflags', '1.3.2'),
+    ('bitflags', '2.4.1'),
+    ('block-buffer', '0.10.4'),
+    ('brotli', '3.4.0'),
+    ('brotli-decompressor', '2.5.1'),
+    ('built', '0.7.1'),
+    ('bumpalo', '3.14.0'),
+    ('bytemuck', '1.14.0'),
+    ('bytemuck_derive', '1.5.0'),
+    ('bytes', '1.5.0'),
+    ('bytes-utils', '0.1.4'),
+    ('cargo-lock', '9.0.0'),
+    ('casey', '0.4.0'),
+    ('cast', '0.3.0'),
+    ('cc', '1.0.83'),
+    ('cfg-if', '1.0.0'),
+    ('chrono', '0.4.31'),
+    ('chrono-tz', '0.8.4'),
+    ('chrono-tz-build', '0.2.1'),
+    ('ciborium', '0.2.1'),
+    ('ciborium-io', '0.2.1'),
+    ('ciborium-ll', '0.2.1'),
+    ('clap', '4.4.11'),
+    ('clap_builder', '4.4.11'),
+    ('clap_lex', '0.6.0'),
+    ('cmake', '0.1.50'),
+    ('comfy-table', '7.1.0'),
+    ('const-oid', '0.9.5'),
+    ('const-random', '0.1.17'),
+    ('const-random-macro', '0.1.16'),
+    ('core-foundation', '0.9.4'),
+    ('core-foundation-sys', '0.8.6'),
+    ('core2', '0.4.0'),
+    ('cpufeatures', '0.2.11'),
+    ('crc', '2.1.0'),
+    ('crc-catalog', '1.1.1'),
+    ('crc32c', '0.6.4'),
+    ('crc32fast', '1.3.2'),
+    ('criterion', '0.5.1'),
+    ('criterion-plot', '0.5.0'),
+    ('crossbeam-channel', '0.5.9'),
+    ('crossbeam-deque', '0.8.4'),
+    ('crossbeam-epoch', '0.9.16'),
+    ('crossbeam-queue', '0.3.9'),
+    ('crossbeam-utils', '0.8.17'),
+    ('crossterm', '0.27.0'),
+    ('crossterm_winapi', '0.9.1'),
+    ('crunchy', '0.2.2'),
+    ('crypto-bigint', '0.4.9'),
+    ('crypto-bigint', '0.5.5'),
+    ('crypto-common', '0.1.6'),
+    ('dary_heap', '0.3.6'),
+    ('der', '0.6.1'),
+    ('deranged', '0.3.10'),
+    ('digest', '0.10.7'),
+    ('doc-comment', '0.3.3'),
+    ('dyn-clone', '1.0.16'),
+    ('ecdsa', '0.14.8'),
+    ('either', '1.9.0'),
+    ('elliptic-curve', '0.12.3'),
+    ('encoding_rs', '0.8.33'),
+    ('enum_dispatch', '0.3.12'),
+    ('env_logger', '0.8.4'),
+    ('equivalent', '1.0.1'),
+    ('errno', '0.3.8'),
+    ('ethnum', '1.5.0'),
+    ('fallible-streaming-iterator', '0.1.9'),
+    ('fast-float', '0.2.0'),
+    ('fastrand', '2.0.1'),
+    ('ff', '0.12.1'),
+    ('flate2', '1.0.28'),
+    ('float-cmp', '0.9.0'),
+    ('fnv', '1.0.7'),
+    ('foreign_vec', '0.1.0'),
+    ('form_urlencoded', '1.2.1'),
+    ('futures', '0.3.29'),
+    ('futures-channel', '0.3.29'),
+    ('futures-core', '0.3.29'),
+    ('futures-executor', '0.3.29'),
+    ('futures-io', '0.3.29'),
+    ('futures-macro', '0.3.29'),
+    ('futures-sink', '0.3.29'),
+    ('futures-task', '0.3.29'),
+    ('futures-util', '0.3.29'),
+    ('generic-array', '0.14.7'),
+    ('getrandom', '0.2.11'),
+    ('gimli', '0.28.1'),
+    ('git2', '0.18.1'),
+    ('glob', '0.3.1'),
+    ('group', '0.12.1'),
+    ('h2', '0.3.22'),
+    ('half', '1.8.2'),
+    ('half', '2.3.1'),
+    ('halfbrown', '0.2.4'),
+    ('hash_hasher', '2.0.3'),
+    ('hashbrown', '0.13.2'),
+    ('hashbrown', '0.14.3'),
+    ('heck', '0.4.1'),
+    ('hermit-abi', '0.3.3'),
+    ('hex', '0.4.3'),
+    ('hmac', '0.12.1'),
+    ('home', '0.5.5'),
+    ('http', '0.2.11'),
+    ('http-body', '0.4.6'),
+    ('httparse', '1.8.0'),
+    ('httpdate', '1.0.3'),
+    ('humantime', '2.1.0'),
+    ('hyper', '0.14.27'),
+    ('hyper-rustls', '0.24.2'),
+    ('iana-time-zone', '0.1.58'),
+    ('iana-time-zone-haiku', '0.1.2'),
+    ('idna', '0.5.0'),
+    ('indexmap', '2.1.0'),
+    ('indoc', '2.0.4'),
+    ('inventory', '0.3.13'),
+    ('ipnet', '2.9.0'),
+    ('is-terminal', '0.4.9'),
+    ('itertools', '0.10.5'),
+    ('itertools', '0.11.0'),
+    ('itoa', '1.0.10'),
+    ('itoap', '1.0.1'),
+    ('jemalloc-sys', '0.5.4+5.3.0-patched'),
+    ('jemallocator', '0.5.4'),
+    ('jobserver', '0.1.27'),
+    ('js-sys', '0.3.66'),
+    ('jsonpath_lib', '0.3.0', 'https://github.com/ritchie46/jsonpath', '24eaf0b4416edff38a4d1b6b17bc4b9f3f047b4b'),
+    ('lazy_static', '1.4.0'),
+    ('lexical-core', '0.8.5'),
+    ('lexical-parse-float', '0.8.5'),
+    ('lexical-parse-integer', '0.8.6'),
+    ('lexical-util', '0.8.5'),
+    ('lexical-write-float', '0.8.5'),
+    ('lexical-write-integer', '0.8.5'),
+    ('libc', '0.2.151'),
+    ('libflate', '1.4.0'),
+    ('libflate', '2.0.0'),
+    ('libflate_lz77', '1.2.0'),
+    ('libflate_lz77', '2.0.0'),
+    ('libgit2-sys', '0.16.1+1.7.1'),
+    ('libloading', '0.8.1'),
+    ('libm', '0.2.8'),
+    ('libmimalloc-sys', '0.1.35'),
+    ('libz-ng-sys', '1.1.12'),
+    ('libz-sys', '1.1.12'),
+    ('linux-raw-sys', '0.4.12'),
+    ('lock_api', '0.4.11'),
+    ('log', '0.4.20'),
+    ('lz4', '1.24.0'),
+    ('lz4-sys', '1.9.4'),
+    ('matrixmultiply', '0.3.8'),
+    ('md-5', '0.10.6'),
+    ('memchr', '2.6.4'),
+    ('memmap2', '0.7.1'),
+    ('memoffset', '0.9.0'),
+    ('mimalloc', '0.1.39'),
+    ('mime', '0.3.17'),
+    ('miniz_oxide', '0.7.1'),
+    ('mio', '0.8.10'),
+    ('multiversion', '0.7.3'),
+    ('multiversion-macros', '0.7.3'),
+    ('ndarray', '0.15.6'),
+    ('now', '0.1.3'),
+    ('ntapi', '0.4.1'),
+    ('num', '0.4.1'),
+    ('num-bigint', '0.4.4'),
+    ('num-complex', '0.4.4'),
+    ('num-integer', '0.1.45'),
+    ('num-iter', '0.1.43'),
+    ('num-rational', '0.4.1'),
+    ('num-traits', '0.2.17'),
+    ('num_cpus', '1.16.0'),
+    ('numpy', '0.20.0'),
+    ('object', '0.32.1'),
+    ('object_store', '0.8.0'),
+    ('once_cell', '1.19.0'),
+    ('oorandom', '11.1.3'),
+    ('openssl-probe', '0.1.5'),
+    ('outref', '0.5.1'),
+    ('p256', '0.11.1'),
+    ('parking_lot', '0.12.1'),
+    ('parking_lot_core', '0.9.9'),
+    ('parquet-format-safe', '0.2.4'),
+    ('parse-zoneinfo', '0.3.0'),
+    ('percent-encoding', '2.3.1'),
+    ('phf', '0.11.2'),
+    ('phf_codegen', '0.11.2'),
+    ('phf_generator', '0.11.2'),
+    ('phf_shared', '0.11.2'),
+    ('pin-project-lite', '0.2.13'),
+    ('pin-utils', '0.1.0'),
+    ('pkcs8', '0.9.0'),
+    ('pkg-config', '0.3.27'),
+    ('planus', '0.3.1'),
+    ('plotters', '0.3.5'),
+    ('plotters-backend', '0.3.5'),
+    ('plotters-svg', '0.3.5'),
+    ('powerfmt', '0.2.0'),
+    ('ppv-lite86', '0.2.17'),
+    ('proc-macro2', '1.0.70'),
+    ('proptest', '1.4.0'),
+    ('prost', '0.11.9'),
+    ('prost-derive', '0.11.9'),
+    ('pyo3', '0.20.0'),
+    ('pyo3-build-config', '0.20.0'),
+    ('pyo3-built', '0.4.7'),
+    ('pyo3-ffi', '0.20.0'),
+    ('pyo3-macros', '0.20.0'),
+    ('pyo3-macros-backend', '0.20.0'),
+    ('quad-rand', '0.2.1'),
+    ('quick-xml', '0.31.0'),
+    ('quickcheck', '1.0.3'),
+    ('quote', '1.0.33'),
+    ('rand', '0.8.5'),
+    ('rand_chacha', '0.3.1'),
+    ('rand_core', '0.6.4'),
+    ('rand_distr', '0.4.3'),
+    ('rand_regex', '0.15.1'),
+    ('rand_xorshift', '0.3.0'),
+    ('rawpointer', '0.2.1'),
+    ('rayon', '1.8.0'),
+    ('rayon-core', '1.12.0'),
+    ('redox_syscall', '0.4.1'),
+    ('ref-cast', '1.0.21'),
+    ('ref-cast-impl', '1.0.21'),
+    ('regex', '1.10.2'),
+    ('regex-automata', '0.4.3'),
+    ('regex-lite', '0.1.5'),
+    ('regex-syntax', '0.6.29'),
+    ('regex-syntax', '0.8.2'),
+    ('reqwest', '0.11.22'),
+    ('rfc6979', '0.3.1'),
+    ('ring', '0.17.7'),
+    ('rle-decode-fast', '1.0.3'),
+    ('rustc-demangle', '0.1.23'),
+    ('rustc-hash', '1.1.0'),
+    ('rustc_version', '0.4.0'),
+    ('rustix', '0.38.28'),
+    ('rustls', '0.21.10'),
+    ('rustls-native-certs', '0.6.3'),
+    ('rustls-pemfile', '1.0.4'),
+    ('rustls-webpki', '0.101.7'),
+    ('rustversion', '1.0.14'),
+    ('ryu', '1.0.16'),
+    ('same-file', '1.0.6'),
+    ('sample-arrow2', '0.17.1'),
+    ('sample-std', '0.1.1'),
+    ('sample-test', '0.1.1'),
+    ('sample-test-macros', '0.1.1'),
+    ('schannel', '0.1.22'),
+    ('scopeguard', '1.2.0'),
+    ('sct', '0.7.1'),
+    ('sec1', '0.3.0'),
+    ('security-framework', '2.9.2'),
+    ('security-framework-sys', '2.9.1'),
+    ('semver', '1.0.20'),
+    ('seq-macro', '0.3.5'),
+    ('serde', '1.0.193'),
+    ('serde_derive', '1.0.193'),
+    ('serde_json', '1.0.108'),
+    ('serde_spanned', '0.6.4'),
+    ('serde_urlencoded', '0.7.1'),
+    ('sha1', '0.10.6'),
+    ('sha2', '0.10.8'),
+    ('signal-hook-registry', '1.4.1'),
+    ('signature', '1.6.4'),
+    ('simd-json', '0.13.4'),
+    ('simdutf8', '0.1.4'),
+    ('siphasher', '0.3.11'),
+    ('slab', '0.4.9'),
+    ('smallvec', '1.11.2'),
+    ('smartstring', '1.0.1'),
+    ('snafu', '0.7.5'),
+    ('snafu-derive', '0.7.5'),
+    ('snap', '1.1.1'),
+    ('socket2', '0.4.10'),
+    ('socket2', '0.5.5'),
+    ('spin', '0.9.8'),
+    ('spki', '0.6.0'),
+    ('sqlparser', '0.39.0'),
+    ('static_assertions', '1.1.0'),
+    ('streaming-decompression', '0.1.2'),
+    ('streaming-iterator', '0.1.9'),
+    ('strength_reduce', '0.2.4'),
+    ('strum', '0.25.0'),
+    ('strum_macros', '0.25.3'),
+    ('subtle', '2.5.0'),
+    ('syn', '1.0.109'),
+    ('syn', '2.0.41'),
+    ('sysinfo', '0.29.11'),
+    ('system-configuration', '0.5.1'),
+    ('system-configuration-sys', '0.5.0'),
+    ('target-features', '0.1.5'),
+    ('target-lexicon', '0.12.12'),
+    ('tempfile', '3.8.1'),
+    ('thiserror', '1.0.50'),
+    ('thiserror-impl', '1.0.50'),
+    ('time', '0.3.30'),
+    ('time-core', '0.1.2'),
+    ('time-macros', '0.2.15'),
+    ('tiny-keccak', '2.0.2'),
+    ('tinytemplate', '1.2.1'),
+    ('tinyvec', '1.6.0'),
+    ('tinyvec_macros', '0.1.1'),
+    ('tokio', '1.35.0'),
+    ('tokio-macros', '2.2.0'),
+    ('tokio-rustls', '0.24.1'),
+    ('tokio-util', '0.7.10'),
+    ('toml', '0.7.8'),
+    ('toml_datetime', '0.6.5'),
+    ('toml_edit', '0.19.15'),
+    ('tower-service', '0.3.2'),
+    ('tracing', '0.1.40'),
+    ('tracing-attributes', '0.1.27'),
+    ('tracing-core', '0.1.32'),
+    ('try-lock', '0.2.5'),
+    ('typed-builder', '0.16.2'),
+    ('typed-builder-macro', '0.16.2'),
+    ('typenum', '1.17.0'),
+    ('unarray', '0.1.4'),
+    ('unicode-bidi', '0.3.14'),
+    ('unicode-ident', '1.0.12'),
+    ('unicode-normalization', '0.1.22'),
+    ('unicode-reverse', '1.0.8'),
+    ('unicode-segmentation', '1.10.1'),
+    ('unicode-width', '0.1.11'),
+    ('unindent', '0.2.3'),
+    ('untrusted', '0.9.0'),
+    ('url', '2.5.0'),
+    ('urlencoding', '2.1.3'),
+    ('uuid', '1.6.1'),
+    ('value-trait', '0.8.0'),
+    ('vcpkg', '0.2.15'),
+    ('version_check', '0.9.4'),
+    ('vsimd', '0.8.0'),
+    ('walkdir', '2.4.0'),
+    ('want', '0.3.1'),
+    ('wasi', '0.11.0+wasi-snapshot-preview1'),
+    ('wasm-bindgen', '0.2.89'),
+    ('wasm-bindgen-backend', '0.2.89'),
+    ('wasm-bindgen-futures', '0.4.39'),
+    ('wasm-bindgen-macro', '0.2.89'),
+    ('wasm-bindgen-macro-support', '0.2.89'),
+    ('wasm-bindgen-shared', '0.2.89'),
+    ('wasm-streams', '0.3.0'),
+    ('web-sys', '0.3.66'),
+    ('webpki-roots', '0.25.3'),
+    ('winapi', '0.3.9'),
+    ('winapi-i686-pc-windows-gnu', '0.4.0'),
+    ('winapi-util', '0.1.6'),
+    ('winapi-x86_64-pc-windows-gnu', '0.4.0'),
+    ('windows-core', '0.51.1'),
+    ('windows-sys', '0.48.0'),
+    ('windows-sys', '0.52.0'),
+    ('windows-targets', '0.48.5'),
+    ('windows-targets', '0.52.0'),
+    ('windows_aarch64_gnullvm', '0.48.5'),
+    ('windows_aarch64_gnullvm', '0.52.0'),
+    ('windows_aarch64_msvc', '0.48.5'),
+    ('windows_aarch64_msvc', '0.52.0'),
+    ('windows_i686_gnu', '0.48.5'),
+    ('windows_i686_gnu', '0.52.0'),
+    ('windows_i686_msvc', '0.48.5'),
+    ('windows_i686_msvc', '0.52.0'),
+    ('windows_x86_64_gnu', '0.48.5'),
+    ('windows_x86_64_gnu', '0.52.0'),
+    ('windows_x86_64_gnullvm', '0.48.5'),
+    ('windows_x86_64_gnullvm', '0.52.0'),
+    ('windows_x86_64_msvc', '0.48.5'),
+    ('windows_x86_64_msvc', '0.52.0'),
+    ('winnow', '0.5.28'),
+    ('winreg', '0.50.0'),
+    ('xmlparser', '0.13.6'),
+    ('xxhash-rust', '0.8.7'),
+    ('zerocopy', '0.7.31'),
+    ('zerocopy-derive', '0.7.31'),
+    ('zeroize', '1.7.0'),
+    ('zstd', '0.13.0'),
+    ('zstd-safe', '7.0.0'),
+    ('zstd-sys', '2.0.9+zstd.1.5.5'),
+]
+
+builddependencies = [
+    ('maturin', '1.4.0', '-Rust-1.75.0'),
+    ('CMake', '3.26.3'),  # needed by crate libz-ng-sys
+]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('matplotlib', '3.7.2'),
+    ('Arrow', '14.0.1'),
+    ('DeltaLake', '0.15.1'),
+    ('openpyxl', '3.1.2'),
+]
+
+use_pip = True
+use_pip_extras = "deltalake,matplotlib,numpy,openpyxl,pandas,pyarrow"
+sanity_pip_check = True
+download_dep_fail = True
+
+moduleclass = 'data'
diff --git a/235_singleM/smafa.eb b/235_singleM/smafa.eb
new file mode 100644
index 00000000..342d27e7
--- /dev/null
+++ b/235_singleM/smafa.eb
@@ -0,0 +1,235 @@
+easyblock = 'Cargo'
+
+name = 'smafa'
+version = '0.8.0'
+
+homepage = 'https://github.com/wwood/smafa'
+description = 'Biological sequence aligner for pre-aligned sequences.'
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+
+source_urls = ['https://github.com/wwood/smafa/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = [
+    {'v0.8.0.tar.gz': '6f103ecd5cdf36fb61572a757732eeb07e905c61b497fa247c1a8397ee775c2d'},
+    {'addr2line-0.22.0.tar.gz': '6e4503c46a5c0c7844e948c9a4d6acd9f50cccb4de1c48eb9e291ea17470c678'},
+    {'adler-1.0.2.tar.gz': 'f26201604c87b1e01bd3d98f8d5d9a8fcbb815e8cedb41ffccbeb4bf593a35fe'},
+    {'aho-corasick-1.1.3.tar.gz': '8e60d3430d3a69478ad0993f19238d2df97c507009a52b3c10addcd7f6bcb916'},
+    {'anstream-0.6.14.tar.gz': '418c75fa768af9c03be99d17643f93f79bbba589895012a80e3452a19ddda15b'},
+    {'anstyle-1.0.7.tar.gz': '038dfcf04a5feb68e9c60b21c9625a54c2c0616e79b72b0fd87075a056ae1d1b'},
+    {'anstyle-parse-0.2.4.tar.gz': 'c03a11a9034d92058ceb6ee011ce58af4a9bf61491aa7e1e59ecd24bd40d22d4'},
+    {'anstyle-query-1.1.0.tar.gz': 'ad186efb764318d35165f1758e7dcef3b10628e26d41a44bc5550652e6804391'},
+    {'anstyle-wincon-3.0.3.tar.gz': '61a38449feb7068f52bb06c12759005cf459ee52bb4adc1d5a7c4322d716fb19'},
+    {'assert_cli-0.6.3.tar.gz': 'a29ab7c0ed62970beb0534d637a8688842506d0ff9157de83286dacd065c8149'},
+    {'atomic-polyfill-1.0.3.tar.gz': '8cf2bce30dfe09ef0bfaef228b9d414faaf7e563035494d7fe092dba54b300f4'},
+    {'autocfg-1.3.0.tar.gz': '0c4b4d0bd25bd0b74681c0ad21497610ce1b7c91b1022cd21c80c6fbdd9476b0'},
+    {'backtrace-0.3.73.tar.gz': '5cc23269a4f8976d0a4d2e7109211a419fe30e8d88d677cd60b6bc79c5732e0a'},
+    {'bird_tool_utils-0.4.1.tar.gz': '6f5f475a22ef913421b64a8d09fad619d9a3a828a5a7450e9b32ab177aa3df56'},
+    {'bird_tool_utils-man-0.4.0.tar.gz': 'a263d1717fd146db3c9bfc0668f9bf19d9078a79fa2c1ba54f00b6d8702d4e0b'},
+    {'bitflags-2.6.0.tar.gz': 'b048fb63fd8b5923fc5aa7b340d8e156aec7ec02f0c78fa8a6ddc2613f6f71de'},
+    {'buffer-redux-1.0.1.tar.gz': '4c9f8ddd22e0a12391d1e7ada69ec3b0da1914f1cec39c5cf977143c5b2854f5'},
+    {'bytecount-0.6.8.tar.gz': '5ce89b21cab1437276d2650d57e971f9d548a2d9037cc231abdc0562b97498ce'},
+    {'byteorder-1.5.0.tar.gz': '1fd0f2584146f6f2ef48085050886acf353beff7305ebd1ae69500e27c67f64b'},
+    {'bzip2-0.4.4.tar.gz': 'bdb116a6ef3f6c3698828873ad02c3014b3c85cadb88496095628e3ef1e347f8'},
+    {'bzip2-sys-0.1.11+1.0.8.tar.gz': '736a955f3fa7875102d57c82b8cac37ec45224a07fd32d58f9f7a186b6cd4cdc'},
+    {'cargo-husky-1.5.0.tar.gz': '7b02b629252fe8ef6460461409564e2c21d0c8e77e0944f3d189ff06c4e932ad'},
+    {'cc-1.1.5.tar.gz': '324c74f2155653c90b04f25b2a47a8a631360cb908f92a772695f430c7e31052'},
+    {'cfg-if-1.0.0.tar.gz': 'baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd'},
+    {'clap-4.5.9.tar.gz': '64acc1846d54c1fe936a78dc189c34e28d3f5afc348403f28ecf53660b9b8462'},
+    {'clap_builder-4.5.9.tar.gz': '6fb8393d67ba2e7bfaf28a23458e4e2b543cc73a99595511eb207fdb8aede942'},
+    {'clap_lex-0.7.1.tar.gz': '4b82cf0babdbd58558212896d1a4272303a57bdb245c2bf1147185fb45640e70'},
+    {'cobs-0.2.3.tar.gz': '67ba02a97a2bd10f4b59b25c7973101c79642302776489e030cd13cdab09ed15'},
+    {'colorchoice-1.0.1.tar.gz': '0b6a852b24ab71dffc585bcb46eaf7959d175cb865a7152e35b348d1b2960422'},
+    {'colored-1.9.4.tar.gz': '5a5f741c91823341bebf717d4c71bda820630ce065443b58bd1b7451af008355'},
+    {'crc32fast-1.4.2.tar.gz': 'a97769d94ddab943e4510d138150169a2758b5ef3eb191a9ee688de3e23ef7b3'},
+    {'critical-section-1.1.2.tar.gz': '7059fff8937831a9ae6f0fe4d658ffabf58f2ca96aa9dec1c889f936f705f216'},
+    {'difference-2.0.0.tar.gz': '524cbf6897b527295dff137cec09ecf3a05f4fddffd7dfcd1585403449e74198'},
+    {'embedded-io-0.4.0.tar.gz': 'ef1a6892d9eef45c8fa6b9e0086428a2cca8491aca8f787c534a3d6d0bcb3ced'},
+    {'env_logger-0.10.2.tar.gz': '4cd405aab171cb85d6735e5c8d9db038c17d3ca007a4d2c25f337935c3d90580'},
+    {'environment-0.1.1.tar.gz': '1f4b14e20978669064c33b4c1e0fb4083412e40fe56cbea2eae80fd7591503ee'},
+    {'errno-0.3.9.tar.gz': '534c5cf6194dfab3db3242765c03bbe257cf92f22b38f6bc0c58d59108a820ba'},
+    {'failure-0.1.8.tar.gz': 'd32e9bd16cc02eae7db7ef620b392808b89f6a5e16bb3497d159c6b92a0f4f86'},
+    {'failure_derive-0.1.8.tar.gz': 'aa4da3c766cd7a0db8242e326e9e4e081edd567072893ed320008189715366a4'},
+    {'fastrand-2.1.0.tar.gz': '9fc0510504f03c51ada170672ac806f1f105a88aa97a5281117e1ddc3368e51a'},
+    {'flate2-1.0.30.tar.gz': '5f54427cfd1c7829e2a139fcefea601bf088ebca651d2bf53ebc600eac295dae'},
+    {'gimli-0.29.0.tar.gz': '40ecd4077b5ae9fd2e9e169b102c6c330d0605168eb0e8bf79952b256dbefffd'},
+    {'hash32-0.2.1.tar.gz': 'b0c35f58762feb77d74ebe43bdbc3210f09be9fe6742234d573bacc26ed92b67'},
+    {'heapless-0.7.17.tar.gz': 'cdc6457c0eb62c71aac4bc17216026d8410337c4126773b9c5daba343f17964f'},
+    {'hermit-abi-0.3.9.tar.gz': 'd231dfb89cfffdbc30e7fc41579ed6066ad03abda9e567ccafae602b97ec5024'},
+    {'humantime-2.1.0.tar.gz': '9a3a5bfb195931eeb336b2a7b4d761daec841b97f947d34394601737a7bba5e4'},
+    {'is-terminal-0.4.12.tar.gz': 'f23ff5ef2b80d608d61efee834934d862cd92461afc0560dedf493e4c033738b'},
+    {'is_terminal_polyfill-1.70.0.tar.gz': 'f8478577c03552c21db0e2724ffb8986a5ce7af88107e6be5d2ee6e158c12800'},
+    {'itoa-1.0.11.tar.gz': '49f1f14873335454500d59611f1cf4a4b0f786f9ac11f4312a78e4cf2566695b'},
+    {'lazy_static-1.5.0.tar.gz': 'bbd2bcb4c963f2ddae06a2efc7e9f3591312473c50c6685e1f298068316e66fe'},
+    {'libc-0.2.155.tar.gz': '97b3888a4aecf77e811145cadf6eef5901f4782c53886191b2f693f24761847c'},
+    {'linux-raw-sys-0.4.14.tar.gz': '78b3ae25bc7c8c38cec158d1f2757ee79e9b3740fbc7ccf0e59e4b08d793fa89'},
+    {'lock_api-0.4.12.tar.gz': '07af8b9cdd281b7915f413fa73f29ebd5d55d0d3f0155584dade1ff18cea1b17'},
+    {'log-0.4.22.tar.gz': 'a7a70ba024b9dc04c27ea2f0c0548feb474ec5c54bba33a7f72f873a39d07b24'},
+    {'lzma-sys-0.1.20.tar.gz': '5fda04ab3764e6cde78b9974eec4f779acaba7c4e84b36eca3cf77c581b85d27'},
+    {'memchr-2.7.4.tar.gz': '78ca9ab1a0babb1e7d5695e3530886289c18cf2f87ec19a575a0abdce112e3a3'},
+    {'miniz_oxide-0.7.4.tar.gz': 'b8a240ddb74feaf34a79a7add65a741f3167852fba007066dcac1ca548d89c08'},
+    {'needletail-0.5.1.tar.gz': 'db05a5ab397f64070d8c998fa0fbb84e484b81f95752af317dac183a82d9295d'},
+    {'object-0.36.1.tar.gz': '081b846d1d56ddfc18fdf1a922e4f6e07a11768ea1b92dec44e42b72712ccfce'},
+    {'pkg-config-0.3.30.tar.gz': 'd231b230927b5e4ad203db57bbcbee2802f6bce620b1e4a9024a07d94e2907ec'},
+    {'postcard-1.0.8.tar.gz': 'a55c51ee6c0db07e68448e336cf8ea4131a620edefebf9893e759b2d793420f8'},
+    {'proc-macro2-1.0.86.tar.gz': '5e719e8df665df0d1c8fbfd238015744736151d4445ec0836b8e628aae103b77'},
+    {'quote-1.0.36.tar.gz': '0fa76aaf39101c457836aec0ce2316dbdc3ab723cdda1c6bd4e6ad4208acaca7'},
+    {'regex-1.10.5.tar.gz': 'b91213439dad192326a0d7c6ee3955910425f441d7038e0d6933b0aec5c4517f'},
+    {'regex-automata-0.4.7.tar.gz': '38caf58cc5ef2fed281f89292ef23f6365465ed9a41b7a7754eb4e26496c92df'},
+    {'regex-syntax-0.8.4.tar.gz': '7a66a03ae7c801facd77a29370b4faec201768915ac14a721ba36f20bc9c209b'},
+    {'roff-0.1.0.tar.gz': 'e33e4fb37ba46888052c763e4ec2acfedd8f00f62897b630cadb6298b833675e'},
+    {'rustc-demangle-0.1.24.tar.gz': '719b953e2095829ee67db738b3bfa9fa368c94900df327b3f07fe6e794d2fe1f'},
+    {'rustc_version-0.4.0.tar.gz': 'bfa0f585226d2e68097d4f95d113b15b83a82e819ab25717ec0590d9584ef366'},
+    {'rustix-0.38.34.tar.gz': '70dc5ec042f7a43c4a73241207cecc9873a06d45debb38b329f8541d85c2730f'},
+    {'ryu-1.0.18.tar.gz': 'f3cb5ba0dc43242ce17de99c180e96db90b235b8a9fdc9543c96d2209116bd9f'},
+    {'scopeguard-1.2.0.tar.gz': '94143f37725109f92c262ed2cf5e59bce7498c01bcc1502d7b9afe439a4e9f49'},
+    {'semver-1.0.23.tar.gz': '61697e0a1c7e512e84a621326239844a24d8207b4669b41bc18b32ea5cbf988b'},
+    {'serde-1.0.204.tar.gz': 'bc76f558e0cbb2a839d37354c575f1dc3fdc6546b5be373ba43d95f231bf7c12'},
+    {'serde_derive-1.0.204.tar.gz': 'e0cd7e117be63d3c3678776753929474f3b04a43a080c744d6b0ae2a8c28e222'},
+    {'serde_json-1.0.120.tar.gz': '4e0d21c9a8cae1235ad58a00c11cb40d4b1e5c784f1ef2c537876ed6ffd8b7c5'},
+    {'spin-0.9.8.tar.gz': '6980e8d7511241f8acf4aebddbb1ff938df5eebe98691418c4468d0b72a96a67'},
+    {'stable_deref_trait-1.2.0.tar.gz': 'a8f112729512f8e442d81f95a8a7ddf2b7c6b8a1a6f509a95864142b30cab2d3'},
+    {'strsim-0.11.1.tar.gz': '7da8b5736845d9f2fcb837ea5d9e2628564b3b043a70948a3f0b778838c5fb4f'},
+    {'syn-1.0.109.tar.gz': '72b64191b275b66ffe2469e8af2c1cfe3bafa67b529ead792a6d0160888b4237'},
+    {'syn-2.0.71.tar.gz': 'b146dcf730474b4bcd16c311627b31ede9ab149045db4d6088b3becaea046462'},
+    {'synstructure-0.12.6.tar.gz': 'f36bdaa60a83aca3921b5259d5400cbf5e90fc51931376a9bd4a0eb79aa7210f'},
+    {'tempfile-3.10.1.tar.gz': '85b77fafb263dd9d05cbeac119526425676db3784113aa9295c88498cbf8bff1'},
+    {'termcolor-1.4.1.tar.gz': '06794f8f6c5c898b3275aebefa6b8a1cb24cd2c6c79397ab15774837a0bc5755'},
+    {'unicode-ident-1.0.12.tar.gz': '3354b9ac3fae1ff6755cb6db53683adb661634f67557942dea4facebec0fee4b'},
+    {'unicode-xid-0.2.4.tar.gz': 'f962df74c8c05a667b5ee8bcf162993134c104e96440b663c8daa176dc772d8c'},
+    {'utf8parse-0.2.2.tar.gz': '06abde3611657adf66d383f00b093d7faecc7fa57071cce2578660c9f1010821'},
+    {'version-compare-0.1.1.tar.gz': '579a42fc0b8e0c63b76519a339be31bed574929511fa53c1a3acae26eb258f29'},
+    {'winapi-0.3.9.tar.gz': '5c839a674fcd7a98952e593242ea400abe93992746761e38641405d28b00f419'},
+    {'winapi-i686-pc-windows-gnu-0.4.0.tar.gz': 'ac3b87c63620426dd9b991e5ce0329eff545bccbbb34f3be09ff6fb6ab51b7b6'},
+    {'winapi-util-0.1.8.tar.gz': '4d4cc384e1e73b93bafa6fb4f1df8c41695c8a91cf9c4c64358067d15a7b6c6b'},
+    {'winapi-x86_64-pc-windows-gnu-0.4.0.tar.gz': '712e227841d057c1ee1cd2fb22fa7e5a5461ae8e48fa2ca79ec42cfc1931183f'},
+    {'windows-sys-0.52.0.tar.gz': '282be5f36a8ce781fad8c8ae18fa3f9beff57ec1b52cb3de0789201425d9a33d'},
+    {'windows-targets-0.52.6.tar.gz': '9b724f72796e036ab90c1021d4780d4d3d648aca59e491e6b98e725b84e99973'},
+    {'windows_aarch64_gnullvm-0.52.6.tar.gz': '32a4622180e7a0ec044bb555404c800bc9fd9ec262ec147edd5989ccd0c02cd3'},
+    {'windows_aarch64_msvc-0.52.6.tar.gz': '09ec2a7bb152e2252b53fa7803150007879548bc709c039df7627cabbd05d469'},
+    {'windows_i686_gnu-0.52.6.tar.gz': '8e9b5ad5ab802e97eb8e295ac6720e509ee4c243f69d781394014ebfe8bbfa0b'},
+    {'windows_i686_gnullvm-0.52.6.tar.gz': '0eee52d38c090b3caa76c563b86c3a4bd71ef1a819287c19d586d7334ae8ed66'},
+    {'windows_i686_msvc-0.52.6.tar.gz': '240948bc05c5e7c6dabba28bf89d89ffce3e303022809e73deaefe4f6ec56c66'},
+    {'windows_x86_64_gnu-0.52.6.tar.gz': '147a5c80aabfbf0c7d901cb5895d1de30ef2907eb21fbbab29ca94c5b08b1a78'},
+    {'windows_x86_64_gnullvm-0.52.6.tar.gz': '24d5b23dc417412679681396f2b49f3de8c1473deb516bd34410872eff51ed0d'},
+    {'windows_x86_64_msvc-0.52.6.tar.gz': '589f6da84c646204747d1270a2a5661ea66ed1cced2631d546fdfb155959f9ec'},
+    {'xz2-0.1.7.tar.gz': '388c44dc09d76f1536602ead6d325eb532f5c122f17782bd57fb47baeeb767e2'},
+]
+
+builddependencies = [
+    ('Rust', '1.75.0'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/%(namelower)s'],
+    'dirs': [],
+}
+
+sanity_check_commands = ["%(namelower)s --help"]
+
+crates = [
+    ('addr2line', '0.22.0'),
+    ('adler', '1.0.2'),
+    ('aho-corasick', '1.1.3'),
+    ('anstream', '0.6.14'),
+    ('anstyle', '1.0.7'),
+    ('anstyle-parse', '0.2.4'),
+    ('anstyle-query', '1.1.0'),
+    ('anstyle-wincon', '3.0.3'),
+    ('assert_cli', '0.6.3'),
+    ('atomic-polyfill', '1.0.3'),
+    ('autocfg', '1.3.0'),
+    ('backtrace', '0.3.73'),
+    ('bird_tool_utils', '0.4.1'),
+    ('bird_tool_utils-man', '0.4.0'),
+    ('bitflags', '2.6.0'),
+    ('buffer-redux', '1.0.1'),
+    ('bytecount', '0.6.8'),
+    ('byteorder', '1.5.0'),
+    ('bzip2', '0.4.4'),
+    ('bzip2-sys', '0.1.11+1.0.8'),
+    ('cargo-husky', '1.5.0'),
+    ('cc', '1.1.5'),
+    ('cfg-if', '1.0.0'),
+    ('clap', '4.5.9'),
+    ('clap_builder', '4.5.9'),
+    ('clap_lex', '0.7.1'),
+    ('cobs', '0.2.3'),
+    ('colorchoice', '1.0.1'),
+    ('colored', '1.9.4'),
+    ('crc32fast', '1.4.2'),
+    ('critical-section', '1.1.2'),
+    ('difference', '2.0.0'),
+    ('embedded-io', '0.4.0'),
+    ('env_logger', '0.10.2'),
+    ('environment', '0.1.1'),
+    ('errno', '0.3.9'),
+    ('failure', '0.1.8'),
+    ('failure_derive', '0.1.8'),
+    ('fastrand', '2.1.0'),
+    ('flate2', '1.0.30'),
+    ('gimli', '0.29.0'),
+    ('hash32', '0.2.1'),
+    ('heapless', '0.7.17'),
+    ('hermit-abi', '0.3.9'),
+    ('humantime', '2.1.0'),
+    ('is-terminal', '0.4.12'),
+    ('is_terminal_polyfill', '1.70.0'),
+    ('itoa', '1.0.11'),
+    ('lazy_static', '1.5.0'),
+    ('libc', '0.2.155'),
+    ('linux-raw-sys', '0.4.14'),
+    ('lock_api', '0.4.12'),
+    ('log', '0.4.22'),
+    ('lzma-sys', '0.1.20'),
+    ('memchr', '2.7.4'),
+    ('miniz_oxide', '0.7.4'),
+    ('needletail', '0.5.1'),
+    ('object', '0.36.1'),
+    ('pkg-config', '0.3.30'),
+    ('postcard', '1.0.8'),
+    ('proc-macro2', '1.0.86'),
+    ('quote', '1.0.36'),
+    ('regex', '1.10.5'),
+    ('regex-automata', '0.4.7'),
+    ('regex-syntax', '0.8.4'),
+    ('roff', '0.1.0'),
+    ('rustc-demangle', '0.1.24'),
+    ('rustc_version', '0.4.0'),
+    ('rustix', '0.38.34'),
+    ('ryu', '1.0.18'),
+    ('scopeguard', '1.2.0'),
+    ('semver', '1.0.23'),
+    ('serde', '1.0.204'),
+    ('serde_derive', '1.0.204'),
+    ('serde_json', '1.0.120'),
+    ('spin', '0.9.8'),
+    ('stable_deref_trait', '1.2.0'),
+    ('strsim', '0.11.1'),
+    ('syn', '1.0.109'),
+    ('syn', '2.0.71'),
+    ('synstructure', '0.12.6'),
+    ('tempfile', '3.10.1'),
+    ('termcolor', '1.4.1'),
+    ('unicode-ident', '1.0.12'),
+    ('unicode-xid', '0.2.4'),
+    ('utf8parse', '0.2.2'),
+    ('version-compare', '0.1.1'),
+    ('winapi', '0.3.9'),
+    ('winapi-i686-pc-windows-gnu', '0.4.0'),
+    ('winapi-util', '0.1.8'),
+    ('winapi-x86_64-pc-windows-gnu', '0.4.0'),
+    ('windows-sys', '0.52.0'),
+    ('windows-targets', '0.52.6'),
+    ('windows_aarch64_gnullvm', '0.52.6'),
+    ('windows_aarch64_msvc', '0.52.6'),
+    ('windows_i686_gnu', '0.52.6'),
+    ('windows_i686_gnullvm', '0.52.6'),
+    ('windows_i686_msvc', '0.52.6'),
+    ('windows_x86_64_gnu', '0.52.6'),
+    ('windows_x86_64_gnullvm', '0.52.6'),
+    ('windows_x86_64_msvc', '0.52.6'),
+    ('xz2', '0.1.7'),
+]
+
+moduleclass = 'bio'
diff --git a/357_Synthcity/synthcity.eb b/357_Synthcity/synthcity.eb
index aad4e563..482faf2d 100644
--- a/357_Synthcity/synthcity.eb
+++ b/357_Synthcity/synthcity.eb
@@ -378,6 +378,7 @@ sanity_check_commands = [
 moduleclass = 'lib'
 
 # ERROR5:
+    # from pytest:
     # twisted 24.3.0 requires automat, ok
     # twisted 24.3.0 requires constantly, ok
     # twisted 24.3.0 requires hyperlink, ok