From 585df50a6d5efd5aa7adbf5829bbc3bb9208f3af Mon Sep 17 00:00:00 2001
From: Jo Hausmann <35309108+johausmann@users.noreply.github.com>
Date: Thu, 26 Oct 2023 12:46:43 +0200
Subject: [PATCH] Update .gitlab-ci.yml

Updated docker container to use mamba instead of conda
---
 .gitlab-ci.yml | 20 ++++++++++++++++----
 1 file changed, 16 insertions(+), 4 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 3a7d0e6..a3ed871 100755
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -8,11 +8,23 @@ before_script:
   #- pip3 install biopython==1.76
   - wget -qO- https://get.nextflow.io | bash && cp nextflow /usr/local/bin/nextflow
   - nextflow help
-  - wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
+  - wget -q https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh
   - mkdir /root/.conda
-  - bash Miniconda3-latest-Linux-x86_64.sh -b && cp /root/miniconda3/bin/* /usr/local/bin/
-  - rm -f Miniconda3-latest-Linux-x86_64.sh
-  - conda --version
+  - bash Mambaforge-Linux-x86_64.sh -b -p /usr/local/bin/conda
+  - rm -f Mambaforge-Linux-x86_64.sh
+  - source /usr/local/bin/conda/etc/profile.d/conda.sh
+  - source /usr/local/bin/conda/etc/profile.d/mamba.sh
+  - which mamba 
+  - mamba --version
+  # this is a workaround for https://github.com/mamba-org/mamba/issues/1993
+  - echo "use_lockfiles:" >> ~/.condarc
+  - echo "  - false" >> ~/.condarc
+  - echo "channels:" >> ~/.condarc
+  - echo "  - defaults" >> ~/.condarc
+  - echo "  - conda-forge" >> ~/.condarc
+  - echo "  - bioconda" >> ~/.condarc
+  - cat ~/.condarc
+
 
 stages:
   - test