docker setup upgraded to work with latest 'docker compose'; not limit…

…ing to 1000 kmers for sacCer3
pritykinlab · Aug 24, 2024 · 213334f · 213334f
1 parent f219674
commit 213334f
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Showing 2 changed files with 5 additions and 2 deletions.
diff --git a/docker/docker-compose.yml b/docker/docker-compose.yml
@@ -7,7 +7,9 @@ services:
     volumes:
       - guidescan_postgres_data:/var/lib/postgresql/data
     environment:
-      - GUIDESCAN_GUIDESCAN_DB=postgresql+psycopg2://${POSTGRES_USER}:${POSTGRES_PASSWORD}@localhost/${POSTGRES_DB}
+      - POSTGRES_USER=${POSTGRES_USER}
+      - POSTGRES_PASSWORD=${POSTGRES_PASSWORD}
+      - POSTGRES_DB=${POSTGRES_DB}
     ports:
       - "5433:5432"
     healthcheck:
@@ -21,7 +23,7 @@ services:
         condition: service_healthy
     volumes:
       - guidescan_data:/data
-    command: snakemake --use-conda --conda-frontend conda --cores 1 --config output_dir="/data" max_kmers=1000 organisms=[\"sacCer3\"] enzymes=[\"cas9\"]
+    command: snakemake --use-conda --conda-frontend conda --cores 1 --config output_dir="/data" organisms=[\"sacCer3\"] enzymes=[\"cas9\"]
     environment:
       - GUIDESCAN_GUIDESCAN_DB=postgresql+psycopg2://${POSTGRES_USER}:${POSTGRES_PASSWORD}@guidescan_db/${POSTGRES_DB}
 

diff --git a/pyproject.toml b/pyproject.toml
@@ -1,3 +1,4 @@
+
 [build-system]
 requires = ["setuptools>=61.0", "setuptools_scm>=6.2"]
 build-backend = "setuptools.build_meta"