#467 working LIQA + working scNanoGPS

vscentrum · Dec 9, 2024 · cbd4b31 · cbd4b31
1 parent 6e3daf1
commit cbd4b31
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Showing 3 changed files with 14 additions and 8 deletions.
diff --git a/467_scNanoGPS/R-bundle-test-gcmr.eb b/467_scNanoGPS/R-bundle-test-gcmr.eb
@@ -52,20 +52,23 @@ exts_list = [
     ('gcmr', '1.0.3', {
         'checksums': ['75773d5119179f186467d33608e9ce1c030d0755dfd6ff196546884078e89754'],
     }),
+    ('frbs', '3.2-0', {
+        'checksums': ['48505d415e3687afcb837e162b63b74173b3cd5df5f96140240e441c86343b2e'],
+    }),
 ]
 
 modextrapaths = {'R_LIBS_SITE': ''}
 
 sanity_check_paths = {
     'files': [],
-    'dirs': ['gcmr'],
+    'dirs': ['gcmr', 'frbs'],
 }
 
 # sanity_check_paths = {
 #     'files': [],
 #     'dirs': ['abind', 'base64', 'calibrate'],
 # }
 
-sanity_check_commands = ['Rscript -e "library(gcmr)"']
+sanity_check_commands = ['Rscript -e "library(gcmr)"', 'Rscript -e "library(frbs)"']
 
 moduleclass = 'lang'
diff --git a/467_scNanoGPS/liqa.eb b/467_scNanoGPS/liqa.eb
@@ -1,14 +1,14 @@
 easyblock = 'PythonPackage'
 
-name = 'Liqa'
+name = 'LIQA'
 version = '1.3.4'
 
 homepage = "https://pypi.org/project/liqa/"
 description = """LIQA (Long-read Isoform Quantification and Analysis) is an Expectation-Maximization
 based statistical method to quantify isoform expression and detect differential alternative splicing (DAS)
 events using long-read RNA-seq data."""
 
-toolchain = {'name': 'gfbf', 'version': '2023a'}
+toolchain = {'name': 'foss', 'version': '2023a'}
 
 sources = [SOURCELOWER_TAR_GZ]
 checksums = ['f8b2e6f0226d99f513d17be3758e6b3e2e9b7b40579f840d28737e827358850e']
@@ -30,12 +30,15 @@ dependencies = [
     ('Pysam', '0.22.0'),
     ('lifelines', '0.28.0'),
     ('R', '4.3.2'),
-    ('R-bundle-CRAN', '2023.12'),
+    # ('R-bundle-CRAN', '2023.12'),
+    ('R-bundle-CRAN-test-gcmr', '2023.12'),
 ]
 
 use_pip = True
-sanity_pip_check = True
 download_dep_fail = True
+sanity_pip_check = True
+
+options = {'modulename': '%(namelower)s_src'}
 
 sanity_check_commands = ['liqa -h']
 

diff --git a/467_scNanoGPS/scNanoGPS_v2.eb b/467_scNanoGPS/scNanoGPS_v2.eb
@@ -59,7 +59,7 @@ dependencies = [
     ('Longshot', '1.0.0'),
     ('BCFtools', '1.21'),
     ('gffread', '0.12.7'),
-    ('Liqa', '1.3.4'),
+    ('LIQA', '1.3.4'),
     # ('lifelines', '0.28.0'),
     # ('R', '4.3.2'),
     # ('R-bundle-CRAN', '2023.12'),
@@ -71,7 +71,7 @@ exts_default_options = {
     'source_urls': [PYPI_SOURCE],
     'download_dep_fail': True,
     'use_pip': True,
-    # 'sanity_pip_check': False,
+    'sanity_pip_check': True,
 }
 
 exts_list = [