Work update + closes #16

vscentrum · Sep 19, 2023 · 2dfe590 · 2dfe590
1 parent 8d28dce
commit 2dfe590
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Showing 37 changed files with 48,882 additions and 744,093 deletions.
diff --git a/169_Bonito/Bonito-0.4.0-fosscuda-2020b.eb b/169_Bonito/Bonito-0.4.0-fosscuda-2020b.eb
@@ -25,7 +25,7 @@ dependencies = [
     ('CuPy', '12.1.0', '-CUDA-%(cudaver)s'),
     ('GenomeWorks', '2021.02.2'),
     ('pyspoa', '0.0.9'),
-    ('ont-fast5-api', '3.3.0'),
+    ('ont-fast5-api', '4.1.1'),
     ('ont-remora', '2.1.2'),
     ('Pysam', '0.20.0'),
     ('pod5-file-format', '0.1.8'),
@@ -106,6 +106,7 @@ exts_list = [
     ('networkx', '2.5.1', {
         'checksums': ['109cd585cac41297f71103c3c42ac6ef7379f29788eb54cb751be5a663bb235a'],
     }),
+    ('ont-koi', '0.3.0', {}),
     ('ont-bonito', version, {
         'modulename': 'bonito',
         'preinstallopts': local_bonito_preinstallopts,

diff --git a/169_Bonito/ont-remora/ONNX-1.11.0-foss-2021a.eb b/169_Bonito/ont-remora/ONNX-1.11.0-foss-2021a.eb
@@ -29,8 +29,8 @@ dependencies = [
 
 use_pip = True
 download_dep_fail = True
-
-preinstallopts = 'env MAX_JOBS="%(parallel)s"'
+prebuildopts = 'sed -i "s|protobuf >=|protobuf <=|g" requirements.txt && '
+preinstallopts = 'env MAX_JOBS="%(parallel)s "'
 
 sanity_check_paths = {
     'files': ['bin/check-model', 'bin/check-node', 'bin/backend-test-tools'],

diff --git a/16_Yambo/2022a/PETSc-3.17.4-intel-2022a.eb b/16_Yambo/2022a/PETSc-3.17.4-intel-2022a.eb
diff --git a/16_Yambo/2022a/configure.log b/16_Yambo/2022a/configure.log
diff --git a/16_Yambo/PETSc.eb b/16_Yambo/PETSc.eb
diff --git a/16_Yambo/SLEPc-3.15.1-foss-2021a.eb b/16_Yambo/SLEPc-3.15.1-foss-2021a.eb
diff --git a/16_Yambo/SuiteSparse.eb b/16_Yambo/SuiteSparse.eb
diff --git a/16_Yambo/SuiteSparse.eb.bak_20230330215238_1347248 b/16_Yambo/SuiteSparse.eb.bak_20230330215238_1347248
diff --git a/16_Yambo/Yambo copy.eb b/16_Yambo/Yambo copy.eb
diff --git a/16_Yambo/Yambo-5.1.2-intel-2021b.eb b/16_Yambo/Yambo-5.1.2-intel-2021b.eb