diff --git a/467_scNanoGPS/Liqa.eb b/467_scNanoGPS/liqa.eb similarity index 86% rename from 467_scNanoGPS/Liqa.eb rename to 467_scNanoGPS/liqa.eb index 416b15b1..c7a5040f 100644 --- a/467_scNanoGPS/Liqa.eb +++ b/467_scNanoGPS/liqa.eb @@ -10,6 +10,9 @@ events using long-read RNA-seq data.""" toolchain = {'name': 'gfbf', 'version': '2023a'} +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f8b2e6f0226d99f513d17be3758e6b3e2e9b7b40579f840d28737e827358850e'] + # Liqa deps: # OK Python # OK Pysam @@ -34,4 +37,6 @@ use_pip = True sanity_pip_check = True download_dep_fail = True +sanity_check_commands = ['liqa -h'] + moduleclass = 'bio' diff --git a/467_scNanoGPS/scNanoGPS_v2.eb b/467_scNanoGPS/scNanoGPS_v2.eb index 7be3f1e3..5604de89 100644 --- a/467_scNanoGPS/scNanoGPS_v2.eb +++ b/467_scNanoGPS/scNanoGPS_v2.eb @@ -59,9 +59,10 @@ dependencies = [ ('Longshot', '1.0.0'), ('BCFtools', '1.21'), ('gffread', '0.12.7'), - ('lifelines', '0.28.0'), - ('R', '4.3.2'), - ('R-bundle-CRAN', '2023.12'), + ('Liqa', '1.3.4'), + # ('lifelines', '0.28.0'), + # ('R', '4.3.2'), + # ('R-bundle-CRAN', '2023.12'), # annovar ] @@ -74,22 +75,22 @@ exts_default_options = { } exts_list = [ - ('liqa', '1.3.4', { - 'modulename': False, - 'checksums': ['f8b2e6f0226d99f513d17be3758e6b3e2e9b7b40579f840d28737e827358850e'], - }), + # ('liqa', '1.3.4', { + # 'modulename': False, + # 'checksums': ['f8b2e6f0226d99f513d17be3758e6b3e2e9b7b40579f840d28737e827358850e'], + # }), ('Distance', '0.1.3', { 'checksums': ['60807584f5b6003f5c521aa73f39f51f631de3be5cccc5a1d67166fcbf0d4551'], }), ] sanity_check_paths = { - 'files': ['bin/liqa'], + 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } sanity_check_commands = [ - "liqa -h", + 'liqa -h', "python -c 'import distance'", "python other_utils/read_length_profiler.py -h", "python scanner.py -h",