diff --git a/variantgrid/settings/components/default_settings.py b/variantgrid/settings/components/default_settings.py index 7f9bbb0a1..9c2923b64 100644 --- a/variantgrid/settings/components/default_settings.py +++ b/variantgrid/settings/components/default_settings.py @@ -421,7 +421,7 @@ LIFTOVER_TO_CHROMOSOMES_ONLY = True # False = Liftover to alt/patches LIFTOVER_DBSNP_ENABLED = False # Default=False - doesn't work so well due to dbSNP IDs being for loci -LIFTOVER_BCFTOOLS_ENABLED = False +LIFTOVER_BCFTOOLS_ENABLED = True LIFTOVER_BCFTOOLS_PLUGIN_DIR = "/usr/share/bcftools/plugins" BCFTOOLS_COMMAND = "bcftools" # if not absolute, needs to be in path diff --git a/variantgrid/settings/env/sharianttest.py b/variantgrid/settings/env/sharianttest.py index a312801aa..d5600d5fe 100644 --- a/variantgrid/settings/env/sharianttest.py +++ b/variantgrid/settings/env/sharianttest.py @@ -26,12 +26,11 @@ _ANNOTATION_BASE_DIR = "/data/annotation" # Set this to where you downloaded annotation (${ANNOTATION_BASE_DIR} from wiki) ANNOTATION_VCF_DUMP_DIR = os.path.join(_ANNOTATION_BASE_DIR, 'test_annotation_scratch') -# LIFTOVER_BCFTOOLS_ENABLED = True - SHARIANT_STATIC_FILES_DIR = os.path.join(VARIANTGRID_APP_DIR, "static_files", "shariant_static") SHARIANT_TEST_STATIC_FILES_DIR = os.path.join(VARIANTGRID_APP_DIR, "static_files", "shariant_test_static") STATICFILES_DIRS = (SHARIANT_TEST_STATIC_FILES_DIR, SHARIANT_STATIC_FILES_DIR,) + STATICFILES_DIRS SHARIANT_TEMPLATES_DIR = os.path.join(VARIANTGRID_APP_DIR, "templates/shariant_templates") TEMPLATES[0]["DIRS"].insert(0, SHARIANT_TEMPLATES_DIR) -VARIANT_SYMBOLIC_ALT_ENABLED = True \ No newline at end of file +VARIANT_SYMBOLIC_ALT_ENABLED = True +HGVS_DEFAULT_METHOD = "biocommons_hgvs" \ No newline at end of file