progress on #236 NGSpeciesID

vscentrum · Feb 7, 2024 · 4d8b5ba · 4d8b5ba
1 parent 0b64807
commit 4d8b5ba
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Showing 11 changed files with 3 additions and 349 deletions.
diff --git a/236_NGSpeciesID/NGSpeciesID-0.3.0-foss-2022b.eb b/236_NGSpeciesID/NGSpeciesID-0.3.0-foss-2022b.eb
diff --git 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
diff --git a/236_NGSpeciesID/WhatsHap-2.1-foss-2022b.eb b/236_NGSpeciesID/WhatsHap-2.1-foss-2022b.eb
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
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
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
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
@@ -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
diff --git 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
Original file line number	Diff line number	Diff line change
Expand Up		@@ -32,5 +32,3 @@ sanity_pip_check = True
		options = {'modulename': _modname}

		moduleclass = 'bio'

		# TODO intervaltree 3.1.0 requires sortedcontainers, which is not installed.