fixed #25

databio · Dec 7, 2023 · 3265306 · 3265306
1 parent f5b82f4
commit 3265306
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Showing 2 changed files with 3 additions and 1 deletion.
diff --git a/bedboss/bedmaker/bedmaker.py b/bedboss/bedmaker/bedmaker.py
@@ -34,6 +34,7 @@
     BED_TO_BIGBED_PROGRAM,
     BIGBED_TO_BED_PROGRAM,
     QC_FOLDER_NAME,
+    REFGENIE_ENV_VAR,
 )
 
 _LOGGER = logging.getLogger("bedboss")
@@ -390,7 +391,7 @@ def get_rgc(self) -> str:
         """
         if not self.rfg_config:
             _LOGGER.info("Creating refgenie genome config file...")
-            cwd = os.getcwd()
+            cwd = os.getenv(REFGENIE_ENV_VAR, os.getcwd())
             self.rfg_config = os.path.join(cwd, "genome_config.yaml")
 
         # get path to the genome config; from arg or env var if arg not provided

diff --git a/bedboss/const.py b/bedboss/const.py
@@ -53,3 +53,4 @@
 DEFAULT_BEDBASE_CACHE_PATH = "./bedabse_cache"
 
 BEDBOSS_PEP_SCHEMA_PATH = "https://schema.databio.org/pipelines/bedboss.yaml"
+REFGENIE_ENV_VAR = "REFGENIE"