issue - SACGF/variantgrid_private#3688 - enable bcftools / biocommons…

… for Shariant test
SACGF · Aug 9, 2024 · c571783 · c571783
1 parent 1aac030
commit c571783
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Showing 2 changed files with 3 additions and 4 deletions.
diff --git 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
@@ -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
+VARIANT_SYMBOLIC_ALT_ENABLED = True
+HGVS_DEFAULT_METHOD = "biocommons_hgvs"