fix -- use cst env var

cancervariants · Aug 7, 2024 · 4b66a7d · 4b66a7d
1 parent a352815
commit 4b66a7d
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Showing 2 changed files with 4 additions and 2 deletions.
diff --git a/server/pyproject.toml b/server/pyproject.toml
@@ -49,6 +49,7 @@ dev = [
     "pre-commit>=3.7.1",
     "gene-normalizer ~= 0.1.39",
     "pydantic-to-typescript",
+    "cool-seq-tool >= 0.4.1"
 ]
 
 [project.scripts]

diff --git a/server/src/curfu/devtools/build_gene_suggest.py b/server/src/curfu/devtools/build_gene_suggest.py
@@ -7,10 +7,11 @@
 
 import click
 from biocommons.seqrepo.seqrepo import SeqRepo
+from cool_seq_tool.handlers.seqrepo_access import SEQREPO_ROOT_DIR
 from gene.database import create_db
 from gene.schemas import RecordType
 
-from curfu import APP_ROOT, SEQREPO_DATA_PATH, logger
+from curfu import APP_ROOT, logger
 
 
 class GeneSuggestionBuilder:
@@ -22,7 +23,7 @@ class GeneSuggestionBuilder:
     def __init__(self) -> None:
         """Initialize class."""
         self.gene_db = create_db()
-        self.sr = SeqRepo(SEQREPO_DATA_PATH)
+        self.sr = SeqRepo(SEQREPO_ROOT_DIR)
         self.genes = []
 
     def _get_chromosome(self, record: dict) -> str | None: