From d057e12ffdd3328246e356968fbd6093b3502170 Mon Sep 17 00:00:00 2001 From: Henry Webel Date: Thu, 16 Oct 2025 14:52:12 +0200 Subject: [PATCH 1/5] =?UTF-8?q?=F0=9F=9A=A7=20Add=20latest=20tags=20to=20b?= =?UTF-8?q?uild=20new=20images?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- Docker/build-push.sh | 4 ++-- modules/environment.yml | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/Docker/build-push.sh b/Docker/build-push.sh index 0b2c043..e63fc91 100644 --- a/Docker/build-push.sh +++ b/Docker/build-push.sh @@ -2,7 +2,7 @@ set -euo pipefail ORG="quay.io/dtu_biosustain_dsp" -VERSION="v0.5.0" +VERSION="v0.5.1" # 1. Build & push the base image (nextflow version) docker buildx build \ @@ -17,4 +17,4 @@ docker buildx build \ --build-arg BASE_VERSION=${VERSION}-nextflow \ --push \ -t ${ORG}/vuegen:${VERSION}-docker \ - -f docker.Dockerfile . \ No newline at end of file + -f docker.Dockerfile . diff --git a/modules/environment.yml b/modules/environment.yml index 5440d23..a7487b4 100644 --- a/modules/environment.yml +++ b/modules/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::vuegen=0.3.2 + - bioconda::vuegen=0.5.1 From 3f48244f79052a9f39ccd32a725c3cdfcb1a441a Mon Sep 17 00:00:00 2001 From: Henry Webel Date: Thu, 16 Oct 2025 15:40:43 +0200 Subject: [PATCH 2/5] :memo: document image updating process a bit --- Docker/REAMDE.md | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 Docker/REAMDE.md diff --git a/Docker/REAMDE.md b/Docker/REAMDE.md new file mode 100644 index 0000000..bab10d1 --- /dev/null +++ b/Docker/REAMDE.md @@ -0,0 +1,31 @@ +# Build images for nextflow + +In order to update the nf-core module of vuegen +([modules/nf-core/vuegen](https://github.com/nf-core/modules/tree/master/modules/nf-core/vuegen)) to a new version, the corresponding docker image needs to be build and pushed to quay.io and then a PR with the updates needs to be submitted to nf-core/modules. + + +## Upload to Quay.io + +Update the container: + - This can be done using the [`build-push.sh`](build-push.sh) script + (after [login to quay.io](https://docs.quay.io/guides/login.html) using `docker login quay.io` + and activating multiplatform builds for your docker driver, e.g. + [docker desktop](https://docs.docker.com/desktop/features/containerd/#enable-the-containerd-image-store).) + - by uploading `nextflow.Dockerfile` (start new build) and specifying a new tag on quay.io itself (being logged-in): + [https://quay.io/repository/dtu_biosustain_dsp/vuegen?tab=builds](quay.io/repository/dtu_biosustain_dsp/vuegen?tab=builds) and + [https://quay.io/repository/dtu_biosustain_dsp/vuegen?tab=tags](quay.io/repository/dtu_biosustain_dsp/vuegen?tab=tags) + +General docs: [https://docs.quay.io/guides/building.html](docs.quay.io/guides/building.html) + + +## Update nf-core module + +Follow the instructions as if you would create a new module: +[https://nf-co.re/docs/tutorials/nf-core_components/components](nf-co.re/docs/tutorials/nf-core_components/components) + +- update `environment.yml` to specify the new version of vuegen on bioconda (this is an automated update) +- update `main.nf` to specify the new version of the container on quay.io (this is a manual update described in the step above) + +Then submit a PR to nf-core/modules, e.g. + +- [https://github.com/nf-core/modules/pull/9201](nf-core/modules/pull/9201) From cc4eb4f4341b6b0fe0c520a3f87f91b6d8a45b9c Mon Sep 17 00:00:00 2001 From: Henry Webel Date: Mon, 27 Oct 2025 09:23:29 +0100 Subject: [PATCH 3/5] :art: dump versions --- modules/VUEGEN.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/VUEGEN.nf b/modules/VUEGEN.nf index 2cdb0ad..3c2bf03 100644 --- a/modules/VUEGEN.nf +++ b/modules/VUEGEN.nf @@ -45,7 +45,7 @@ process VUEGEN { cat <<-END_VERSIONS > versions.yml "${task.process}": - vuegen: \$( vuegen --version | sed -e "s/vuegen //g" ) + vuegen: \$( python -c "import vuegen; print(vuegen.__version__)" ) END_VERSIONS """ @@ -57,7 +57,7 @@ process VUEGEN { cat <<-END_VERSIONS > versions.yml "${task.process}": - vuegen: \$( vuegen --version | sed -e "s/vuegen //g" ) + vuegen: \$( python -c "import vuegen; print(vuegen.__version__)" ) END_VERSIONS """ } From b6792740b176a7752b77efeb905002f605d5d922 Mon Sep 17 00:00:00 2001 From: Henry Webel Date: Mon, 27 Oct 2025 09:23:48 +0100 Subject: [PATCH 4/5] :art: typo --- Docker/nextflow.Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Docker/nextflow.Dockerfile b/Docker/nextflow.Dockerfile index d7cac77..bc83a20 100644 --- a/Docker/nextflow.Dockerfile +++ b/Docker/nextflow.Dockerfile @@ -17,7 +17,7 @@ RUN export DEBIAN_FRONTEND=noninteractive && \ && apt-get clean \ && rm -rf /var/lib/apt/lists/* -# Install vuegen Python packag +# Install vuegen Python package RUN pip install --no-cache-dir -U vuegen # Create and switch to non-root user for security reasons @@ -42,4 +42,4 @@ ENV XDG_RUNTIME_DIR=/tmp \ XDG_CACHE_HOME=/tmp/quarto_cache_home \ XDG_DATA_HOME=/tmp/quarto_data_home \ PATH="${PATH}:/home/appuser/bin" \ - PYTHONFAULTHANDLER=1 \ No newline at end of file + PYTHONFAULTHANDLER=1 From 797363c0b4b8c2c86197bd78c015be798a4c0e6e Mon Sep 17 00:00:00 2001 From: Henry Webel Date: Mon, 27 Oct 2025 09:24:01 +0100 Subject: [PATCH 5/5] =?UTF-8?q?=F0=9F=94=A7=20set=20Python=20version=20exp?= =?UTF-8?q?licitly=20to=203.12?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- modules/environment.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/modules/environment.yml b/modules/environment.yml index a7487b4..bfd765f 100644 --- a/modules/environment.yml +++ b/modules/environment.yml @@ -5,3 +5,4 @@ channels: - bioconda dependencies: - bioconda::vuegen=0.5.1 + - conda-forge::python=3.12