Merge pull request #58 from genomic-medicine-sweden/fix_mamba

Fix mamba error
genomic-medicine-sweden · May 30, 2022 · 75b75c9 · 75b75c9
2 parents c4edf92 + 1a37373
commit 75b75c9
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diff --git a/.github/workflows/build_dockerfile.yml b/.github/workflows/build_dockerfile.yml
@@ -3,6 +3,9 @@ name: Update docker for artic-ncov2019-illumina, artic-ncov2019-nanopore
 on:
  schedule:
    - cron: '0 0 * * *'
+ push:
+    branches:
+      - fix_mamba 
 jobs:
   get-version:
     runs-on: ubuntu-latest

diff --git a/environments/illumina/Dockerfile b/environments/illumina/Dockerfile
@@ -6,6 +6,7 @@ COPY environments/extras.yml /extras.yml
 COPY environments/illumina/environment.yml /environment.yml
 RUN /opt/conda/bin/conda update conda && \
 /opt/conda/bin/conda install mamba -c conda-forge && \
+/opt/conda/bin/conda update mamba -c conda-forge && \
 /opt/conda/bin/mamba env create -f /environment.yml
 
 FROM debian:buster-slim

diff --git a/environments/nanopore/Dockerfile b/environments/nanopore/Dockerfile
@@ -5,6 +5,7 @@ LABEL authors="Matt Bull" \
 COPY environments/extras.yml /extras.yml
 COPY environments/nanopore/environment.yml /environment.yml
 RUN /opt/conda/bin/conda install mamba -c conda-forge && \
+/opt/conda/bin/conda update mamba -c conda-forge && \
 /opt/conda/bin/mamba env create -f /environment.yml
 
 FROM debian:buster-slim