From 9d8ec93ab090e9437a856d0620a0d1963f411c52 Mon Sep 17 00:00:00 2001
From: Samuele Cancellieri
 <32717860+samuelecancellieri@users.noreply.github.com>
Date: Thu, 15 Feb 2024 13:48:17 +0100
Subject: [PATCH] update dockerfile with micromamba and correct package
 versions

---
 Dockerfile | 29 ++++++++++++++---------------
 1 file changed, 14 insertions(+), 15 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index e7b5ed3..a4a0bdf 100755
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,26 +1,25 @@
-# Set the base image to anaconda python 3.8
-FROM continuumio/miniconda3
+# Set the base image to micromamba
+FROM mambaorg/micromamba
 
 # File Author / Maintainer
 # MAINTAINER Samuele Cancelleri
 
-ENV SHELL bash
+# Set the variables for version control during installation
+ARG crispritz_version=2.6.6
+ARG crisprme_version=2.1.2
 
-#update conda channel with bioconda and conda-forge
-RUN conda config --add channels defaults 
-RUN conda config --add channels conda-forge
-RUN conda config --add channels bioconda
+# set the shell to bash
+ENV SHELL bash
+# set user as root
+USER root
 
-#update packages of the docker system
+#update packages of the docker image
 RUN apt-get update && apt-get install gsl-bin libgsl0-dev -y && apt-get install libgomp1 -y && apt-get clean
 RUN apt-get upgrade -y && apt-get clean
 RUN apt update
 RUN apt upgrade -y
 
-#Install crisprme package
-RUN conda update -n base -c defaults conda
-RUN conda update --all -y
-RUN conda install python=3.8 -y
-RUN conda install crispritz -y
-RUN conda install crisprme=2.1.1 -y
-
+# Install crispritz & crisprme packages
+RUN micromamba install -y -n base -c conda-forge -c bioconda python=3.9 crispritz=$crispritz_version crisprme=$crisprme_version && micromamba clean --all --yes
+# Start the base environment
+ARG MAMBA_DOCKERFILE_ACTIVATE=1
\ No newline at end of file