From be970e813a9022260a4ee9e41d3dd4e83b57a9cc Mon Sep 17 00:00:00 2001
From: farchaab <farid.chaabane@chuv.ch>
Date: Wed, 28 Aug 2024 10:37:25 +0200
Subject: [PATCH] install utils and ps with apt

---
 Dockerfile | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index de9ea0d..99eddae 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -3,7 +3,15 @@ LABEL org.opencontainers.image.source=https://github.com/metagenlab/assembly_fin
 LABEL org.opencontainers.image.description="Snakemake-powered cli to download genomes with NCBI datasets"
 LABEL org.opencontainers.image.licenses=MIT
 ENV LANG=C.UTF-8 
-ENV SHELL=/bin/bash 
+ENV SHELL=/bin/bash
+
+USER root
+ENV APT_PKGS="curl rsync p7zip-full procps"
+RUN apt-get update \
+    && apt-get install -y --no-install-recommends ${APT_PKGS} \
+    && apt-get clean \
+    && rm -rf /var/lib/apt /var/lib/dpkg /var/lib/cache /var/lib/log
+USER $MAMBA_USER
 
 COPY --chown=$MAMBA_USER:$MAMBA_USER . /pkg
 RUN micromamba config set extract_threads 1 && \