#467 PR version

vscentrum · Dec 16, 2024 · b96cad7 · b96cad7
1 parent f91b3b8
commit b96cad7
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Showing 2 changed files with 1 addition and 41 deletions.
diff --git a/467_scNanoGPS/liqa.eb b/467_scNanoGPS/liqa.eb
@@ -13,16 +13,6 @@ toolchain = {'name': 'foss', 'version': '2023a'}
 sources = [SOURCELOWER_TAR_GZ]
 checksums = ['f8b2e6f0226d99f513d17be3758e6b3e2e9b7b40579f840d28737e827358850e']
 
-# Liqa deps:
-    # OK Python
-        # OK Pysam
-        # OK Numpy
-        # OK Scipy
-        # OK UPDATED Lifelines - already lifelines in synthcity not used 2023a
-    # OK R
-        # OK ADD_TO_CRAN gcmr
-        # OK betareg
-
 dependencies = [
     ('Python', '3.11.3'),
     ('SciPy-bundle', '2023.07'),

diff --git a/467_scNanoGPS/scNanoGPS_v2.eb b/467_scNanoGPS/scNanoGPS_v2.eb
@@ -12,36 +12,6 @@ source_urls = ['https://github.com/gaolabtools/scNanoGPS/archive/refs/tags/']
 sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}]
 checksums = ['60cce1c771283b6d7a3639aa5744acfd6162306d95dd419ad3c265461fdda218']
 
-# DEPS:
-    # OK - biopython 1.79
-    # ok - distance 0.1.3
-    # OK - matplotlib 3.5.2
-    # OK - pandas 1.4.2
-    # OK - pysam 0.19.0
-    # OK - seaborn 0.11.2
-    # OK minimap2
-    # OK Samtools
-    # OK UPDATED tabix
-    # OK SPOA
-    # OK SubRead featureCounts
-    # ok LIQA
-    # OK Longshot
-    # OK CREATED BFCtools
-    # !!! UPDATE ANNOVAR -> sources are not open -> no sources on hpc -> try to register and download -> 404
-        # it is used in reporter_SNV.py
-    # Optional:
-        # OK gffread
-        # Qualimap - not for 2023a 
-    # Liqa deps: -> separate EC
-        # OK Python
-            # OK Pysam
-            # OK Numpy
-            # OK Scipy
-            # OK UPDATED Lifelines - already lifelines in synthcity not used 2023a
-        # OK R
-            # OK ADD_TO_CRAN gcmr
-            # OK betareg
-
 dependencies = [
     ('Python', '3.11.3'),
     ('Python-bundle-PyPI', '2023.06'),
@@ -60,7 +30,7 @@ dependencies = [
     ('BCFtools', '1.21'),
     ('gffread', '0.12.7'),
     ('LIQA', '1.3.4'),
-    # Optional - load 'annovar/20200607-GCCcore-12.3.0-Perl-5.36.1' to make reporter_SNV.py work
+    # Optional - load 'annovar/20200607-GCCcore-12.3.0-Perl-5.36.1' to make 'reporter_SNV.py' work
 ]
 
 exts_defaultclass = 'PythonPackage'