From 42dc9e54bb5e65624c69ceac0eb64abebd230a06 Mon Sep 17 00:00:00 2001 From: Thomas Cokelaer Date: Thu, 23 Jul 2026 13:49:41 +0200 Subject: [PATCH 1/3] ci: install bcftools explicitly in test workflow bcftools is listed in environment.yml but was missing at test time, likely due to a stale cached environment. Install it explicitly after micromamba setup and verify the binary resolves. --- .github/workflows/main.yml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index dd745dd..f59e668 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -39,6 +39,11 @@ jobs: cache-environment: true cache-downloads: true + - name: install bcftools + run: | + micromamba install -y -n sequana_variant_calling -c conda-forge -c bioconda bcftools + micromamba run -n sequana_variant_calling bcftools --version + - name: install package itself shell: bash -l {0} run: | From bd90fc23a30bcb2cb294578ebc3dba3cfb45eb4f Mon Sep 17 00:00:00 2001 From: Thomas Cokelaer Date: Thu, 23 Jul 2026 14:13:04 +0200 Subject: [PATCH 2/3] ci: disable micromamba environment caching Restored environment caches kept the conda package metadata but lost files on disk, so bcftools was reported as already installed while libgsl.so.25 was missing at runtime. A fresh solve of environment.yml correctly pulls bcftools 1.24 with gsl 2.7, which provides that library. Drop the explicit bcftools install added previously (a no-op against a corrupt env) and replace it with a version check that fails fast. Package download caching is kept. --- .github/workflows/main.yml | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index f59e668..c607438 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -36,13 +36,16 @@ jobs: environment-file: environment.yml create-args: >- python=${{ matrix.python }} - cache-environment: true + # environment caching is disabled on purpose: restored envs kept the + # package metadata but lost files on disk, so bcftools was reported as + # installed while libgsl.so.25 was missing at runtime + cache-environment: false cache-downloads: true - - name: install bcftools + - name: check bcftools + shell: bash -l {0} run: | - micromamba install -y -n sequana_variant_calling -c conda-forge -c bioconda bcftools - micromamba run -n sequana_variant_calling bcftools --version + bcftools --version - name: install package itself shell: bash -l {0} From 902bb1dc35eca9055f77e2f54eb8188a007828f8 Mon Sep 17 00:00:00 2001 From: Thomas Cokelaer Date: Thu, 23 Jul 2026 14:21:42 +0200 Subject: [PATCH 3/3] Fix CI --- doc/index.rst | 7 +++---- environment.yml | 1 + 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/doc/index.rst b/doc/index.rst index bc2905c..7c74018 100644 --- a/doc/index.rst +++ b/doc/index.rst @@ -3,10 +3,10 @@ Sequana variant calling pipeline documentation |version|, |today|, status:production -The **variant_calling** pipeline is a `Sequana `_ pipeline. You can find the source code +The **variant_calling** pipeline is a `Sequana `_ pipeline. You can find the source code on `https://github.com/sequana/sequana_variant_calling `_. Would you have issues -about the code, usage or lack of information, please fill a report -on `Sequana itself `_ indicating the pipeline name (We centralized all +about the code, usage or lack of information, please fill a report +on `Sequana itself `_ indicating the pipeline name (We centralized all pipelines issues on **Sequana** repository only so as to be more responsive). If you use **Sequana**, please do not forget to cite us: @@ -38,4 +38,3 @@ What is Sequana ? To join the project, please let us know on `github `_. For more information, please see `github `_. - diff --git a/environment.yml b/environment.yml index 7f40af2..11c10e3 100644 --- a/environment.yml +++ b/environment.yml @@ -7,6 +7,7 @@ dependencies: - freebayes>1.3 - bwa - bcftools +- gsl - snpeff==5.1d - sambamba - fastp