diff --git a/467_scNanoGPS/R-bundle-test-gcmr.eb b/467_scNanoGPS/R-bundle-test-gcmr.eb index ffdb160c..b6ef4170 100644 --- a/467_scNanoGPS/R-bundle-test-gcmr.eb +++ b/467_scNanoGPS/R-bundle-test-gcmr.eb @@ -52,13 +52,16 @@ 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 = { @@ -66,6 +69,6 @@ sanity_check_paths = { # 'dirs': ['abind', 'base64', 'calibrate'], # } -sanity_check_commands = ['Rscript -e "library(gcmr)"'] +sanity_check_commands = ['Rscript -e "library(gcmr)"', 'Rscript -e "library(frbs)"'] moduleclass = 'lang' \ No newline at end of file diff --git a/467_scNanoGPS/liqa.eb b/467_scNanoGPS/liqa.eb index c7a5040f..347053da 100644 --- a/467_scNanoGPS/liqa.eb +++ b/467_scNanoGPS/liqa.eb @@ -1,6 +1,6 @@ easyblock = 'PythonPackage' -name = 'Liqa' +name = 'LIQA' version = '1.3.4' homepage = "https://pypi.org/project/liqa/" @@ -8,7 +8,7 @@ description = """LIQA (Long-read Isoform Quantification and Analysis) is an Expe 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 index 5604de89..66654964 100644 --- 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 = [