diff --git a/.github/workflows/docker.yaml b/.github/workflows/docker.yaml index 597c2c5e..5030120b 100644 --- a/.github/workflows/docker.yaml +++ b/.github/workflows/docker.yaml @@ -8,9 +8,9 @@ on: # # - master # # on: - # push: - # branches: - # - dev + push: + branches: + - dev env: IMAGE_NAME: mosaicatcher-pipeline diff --git a/github-actions-runner/Dockerfile-2.1.2.dockerfile b/github-actions-runner/Dockerfile-2.1.2.dockerfile index 37120244..de3db142 100644 --- a/github-actions-runner/Dockerfile-2.1.2.dockerfile +++ b/github-actions-runner/Dockerfile-2.1.2.dockerfile @@ -1,6 +1,6 @@ FROM condaforge/mambaforge:latest LABEL io.github.snakemake.containerized="true" -LABEL io.github.snakemake.conda_env_hash="55c177ec267b6cafb7c46af6bd81eceaffe243d4e28a2a2434e5abddc1e8cff0" +LABEL io.github.snakemake.conda_env_hash="b7d5e2bcd141dad41821c6a0d68901d31b2eb5a6bf07407e123bc6eae70af0e8" # Step 1: Retrieve conda environments @@ -154,7 +154,7 @@ COPY workflow/envs/mc_bioinfo_tools.yaml /conda-envs/f251d84cdc9f25d0e14b48e7802 # Conda environment: # source: workflow/envs/rtools.yaml -# prefix: /conda-envs/5eb5026d8b42b407b8711e037d9cc4ff +# prefix: /conda-envs/261d620cc100b901beec2634c6032c4f # name: rtools # channels: # - bioconda @@ -167,9 +167,7 @@ COPY workflow/envs/mc_bioinfo_tools.yaml /conda-envs/f251d84cdc9f25d0e14b48e7802 # # ############### # - bioconductor-biocparallel # - bioconductor-bsgenome -# - bioconductor-bsgenome.hsapiens.ucsc.hg19 # - bioconductor-bsgenome.hsapiens.ucsc.hg38 -# - bioconductor-bsgenome.mmusculus.ucsc.mm10 # - bioconductor-complexheatmap # # - bioconductor-fastseg # - bioconductor-genomicalignments @@ -207,8 +205,8 @@ COPY workflow/envs/mc_bioinfo_tools.yaml /conda-envs/f251d84cdc9f25d0e14b48e7802 # - r-tidyr # - r-ggbeeswarm # - r-pheatmap -RUN mkdir -p /conda-envs/5eb5026d8b42b407b8711e037d9cc4ff -COPY workflow/envs/rtools.yaml /conda-envs/5eb5026d8b42b407b8711e037d9cc4ff/environment.yaml +RUN mkdir -p /conda-envs/261d620cc100b901beec2634c6032c4f +COPY workflow/envs/rtools.yaml /conda-envs/261d620cc100b901beec2634c6032c4f/environment.yaml # Step 2: Generate conda environments @@ -218,10 +216,5 @@ RUN mamba env create --prefix /conda-envs/d7ae7fcf4adb54129dbf1b1e84ef888a --fil mamba env create --prefix /conda-envs/08d4368302a4bdf7eda6b536495efe7d --file /conda-envs/08d4368302a4bdf7eda6b536495efe7d/environment.yaml && \ mamba env create --prefix /conda-envs/c80307395eddf442c2fb6870f40d822b --file /conda-envs/c80307395eddf442c2fb6870f40d822b/environment.yaml && \ mamba env create --prefix /conda-envs/f251d84cdc9f25d0e14b48e780261d66 --file /conda-envs/f251d84cdc9f25d0e14b48e780261d66/environment.yaml && \ - mamba env create --prefix /conda-envs/5eb5026d8b42b407b8711e037d9cc4ff --file /conda-envs/5eb5026d8b42b407b8711e037d9cc4ff/environment.yaml && \ + mamba env create --prefix /conda-envs/261d620cc100b901beec2634c6032c4f --file /conda-envs/261d620cc100b901beec2634c6032c4f/environment.yaml && \ mamba clean --all -y - - -# # Custom Bsgenome R install -# COPY github-actions-runner/bioconductor_install.R /conda-envs/ -# RUN chmod -R 0777 /conda-envs/91d5ffe2d429bcebd6bab78e9ca3a1d4/lib/R/library && /conda-envs/91d5ffe2d429bcebd6bab78e9ca3a1d4/bin/Rscript /conda-envs/bioconductor_install.R diff --git a/workflow/envs/rtools.yaml b/workflow/envs/rtools.yaml index 2ccbffb3..e1580794 100644 --- a/workflow/envs/rtools.yaml +++ b/workflow/envs/rtools.yaml @@ -10,9 +10,7 @@ dependencies: # ############### - bioconductor-biocparallel - bioconductor-bsgenome - - bioconductor-bsgenome.hsapiens.ucsc.hg19 - bioconductor-bsgenome.hsapiens.ucsc.hg38 - - bioconductor-bsgenome.mmusculus.ucsc.mm10 - bioconductor-complexheatmap # - bioconductor-fastseg - bioconductor-genomicalignments