From 7098723a725d9f3a42400565eb6aac14d1fa009b Mon Sep 17 00:00:00 2001 From: Sofia Stamouli Date: Mon, 30 May 2022 12:45:21 +0200 Subject: [PATCH 1/3] Fix mamba error --- .github/workflows/build_dockerfile.yml | 2 ++ environments/illumina/Dockerfile | 1 + environments/nanopore/Dockerfile | 1 + 3 files changed, 4 insertions(+) diff --git a/.github/workflows/build_dockerfile.yml b/.github/workflows/build_dockerfile.yml index 4b6466f1..8947fa2e 100644 --- a/.github/workflows/build_dockerfile.yml +++ b/.github/workflows/build_dockerfile.yml @@ -3,6 +3,8 @@ name: Update docker for artic-ncov2019-illumina, artic-ncov2019-nanopore on: schedule: - cron: '0 0 * * *' + push: + - fix-R-error jobs: get-version: runs-on: ubuntu-latest diff --git a/environments/illumina/Dockerfile b/environments/illumina/Dockerfile index d21e8e62..e34bcbe7 100644 --- 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 index a6aae664..d45eef4d 100644 --- 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 From da98cd61e36c5e65442320e3a5cc8ad291d67259 Mon Sep 17 00:00:00 2001 From: Sofia Stamouli Date: Mon, 30 May 2022 12:47:07 +0200 Subject: [PATCH 2/3] Fix mamba error --- .github/workflows/build_dockerfile.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build_dockerfile.yml b/.github/workflows/build_dockerfile.yml index 8947fa2e..26c21de7 100644 --- a/.github/workflows/build_dockerfile.yml +++ b/.github/workflows/build_dockerfile.yml @@ -4,7 +4,7 @@ on: schedule: - cron: '0 0 * * *' push: - - fix-R-error + - fix_mamba jobs: get-version: runs-on: ubuntu-latest From 1a373730beff1089d3a71a037aee5674059066db Mon Sep 17 00:00:00 2001 From: Sofia Stamouli Date: Mon, 30 May 2022 12:52:32 +0200 Subject: [PATCH 3/3] Fix activity type for workflow --- .github/workflows/build_dockerfile.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/build_dockerfile.yml b/.github/workflows/build_dockerfile.yml index 26c21de7..281eee51 100644 --- a/.github/workflows/build_dockerfile.yml +++ b/.github/workflows/build_dockerfile.yml @@ -4,7 +4,8 @@ on: schedule: - cron: '0 0 * * *' push: - - fix_mamba + branches: + - fix_mamba jobs: get-version: runs-on: ubuntu-latest