progress on #236 NGSpeciesID

vscentrum · Feb 7, 2024 · 32d7245 · 32d7245
1 parent 4d8b5ba
commit 32d7245
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Showing 4 changed files with 45 additions and 38 deletions.
diff --git a/236_NGSpeciesID/Pysam-0.22.0-GCC-12.3.0.eb b/236_NGSpeciesID/Pysam-0.22.0-GCC-12.3.0.eb
diff --git a/236_NGSpeciesID/WhatsHap-2.1-foss-2023a.eb → 236_NGSpeciesID/WhatsHap-2.2-foss-2023a.eb b/236_NGSpeciesID/WhatsHap-2.1-foss-2023a.eb → 236_NGSpeciesID/WhatsHap-2.2-foss-2023a.eb
@@ -1,9 +1,7 @@
-# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
-
 easyblock = 'PythonBundle'
 
 name = 'WhatsHap'
-version = '2.1'
+version = '2.2'
 
 homepage = 'https://whatshap.readthedocs.io'
 description = """WhatsHap is a software for phasing genomic variants using DNA
@@ -21,7 +19,7 @@ dependencies = [
     ('SciPy-bundle', '2023.07'),
     ('Biopython', '1.83'),
     ('Yasm', '1.3.0'),
-    ('pyfaidx', '0.8.0'),
+    ('pyfaidx', '0.8.1.1'),
     ('python-isal', '1.1.0'),
 ]
 
@@ -38,7 +36,7 @@ exts_list = [
         'checksums': ['4a19814a5b0a4392d788ac2315263435293579b0583c3469943fe0c6a586f263'],
     }),
     ('whatshap', version, {
-        'checksums': ['9b61812eda1dd5251ba8d02db16d7ddda152ccc813cb3db6a1ec796f1865fe8d'],
+        'checksums': ['4cd34e9b82930c4f42e9e6b7dce2e321e4c81f934fdb980b6093ad91a06ae30a'],
     }),
 ]
 

diff --git a/236_NGSpeciesID/parasail-2.6.2-GCC-12.3.0.eb b/236_NGSpeciesID/parasail-2.6.2-GCC-12.3.0.eb
@@ -10,7 +10,6 @@ description = """parasail is a SIMD C (C99) library containing implementations
 
 toolchain = {'name': 'GCC', 'version': '12.3.0'}
 
-# https://github.com/jeffdaily/parasail
 github_account = 'jeffdaily'
 source_urls = [GITHUB_SOURCE]
 sources = ['v%(version)s.tar.gz']

diff --git a/236_NGSpeciesID/pyfaidx-0.8.1.1-GCCcore-12.3.0.eb b/236_NGSpeciesID/pyfaidx-0.8.1.1-GCCcore-12.3.0.eb
@@ -0,0 +1,42 @@
+easyblock = 'PythonBundle'
+
+name = 'pyfaidx'
+version = '0.8.1.1'
+
+homepage = 'https://pypi.python.org/pypi/pyfaidx'
+description = "pyfaidx: efficient pythonic random access to fasta subsequences"
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+
+dependencies = [('Python', '3.11.3')]
+
+sanity_pip_check = True
+use_pip = True
+
+exts_list = [
+    ('zipp', '3.17.0', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['0e923e726174922dce09c53c59ad483ff7bbb8e572e00c7f7c46b88556409f31'],
+    }),
+    ('importlib_metadata', '7.0.1', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['4805911c3a4ec7c3966410053e9ec6a1fecd629117df5adee56dfc9432a1081e'],
+    }),
+    (name, version, {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['2694af8e3f35f1890a03f04c0f89ba245caf24ff9e435f2c494b132f537e70f6'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/faidx'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ["faidx --help"]
+
+moduleclass = 'bio'