Re-adding directory creation ad BedTools constructor

dieterich-lab · Jun 24, 2024 · 2ff1e52 · 2ff1e52
1 parent b22d189
commit 2ff1e52
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diff --git a/docker/app_container/Dockerfile b/docker/app_container/Dockerfile
@@ -9,7 +9,7 @@ COPY docker/app_container/files/. /app/
 RUN apt-get update \
     && apt-get install -y bedtools findutils \
     && useradd app \
-    && mkdir -p /uploads /tmp/bedtools /app/venv \
+    && mkdir -p /uploads /app/venv \
     && chown -R app /uploads /install /app/venv \
     && cp -r /install/migrations /install/alembic.ini /app
 

diff --git a/server/src/scimodom/services/bedtools.py b/server/src/scimodom/services/bedtools.py
@@ -1,5 +1,6 @@
 from functools import cache
 import logging
+from os import makedirs
 from pathlib import Path
 from typing import Iterable, Sequence, Any
 
@@ -91,6 +92,7 @@ def _remove_filno(feature, n_fields: int = 9, is_closest: bool = False):
 
 class BedToolsService:
     def __init__(self, tmp_path):
+        makedirs(tmp_path, exist_ok=True)
         pybedtools.helpers.set_tempdir(tmp_path)
 
     def annotate_data_using_ensembl(