From 527b5d00f76e22f7daba203a233802cee8191f79 Mon Sep 17 00:00:00 2001 From: Thomas Weber Date: Tue, 5 Dec 2023 10:44:02 +0000 Subject: [PATCH] Dockerfile --- .../Dockerfile-2.2.4.dockerfile | 300 ++++++++++++++++++ .../add_T2T_part_to_Dockerfile.sh | 1 - 2 files changed, 300 insertions(+), 1 deletion(-) create mode 100644 github-actions-runner/Dockerfile-2.2.4.dockerfile diff --git a/github-actions-runner/Dockerfile-2.2.4.dockerfile b/github-actions-runner/Dockerfile-2.2.4.dockerfile new file mode 100644 index 00000000..f03d13ea --- /dev/null +++ b/github-actions-runner/Dockerfile-2.2.4.dockerfile @@ -0,0 +1,300 @@ +FROM condaforge/mambaforge:latest +LABEL io.github.snakemake.containerized="true" +LABEL io.github.snakemake.conda_env_hash="8c338e2bbe95ae23ac438e1ac650a859ed4dbb9a77747c17f62707ea2f67a667" + +# Step 1: Retrieve conda environments + +# Conda environment: +# source: https://github.com/friendsofstrandseq/ashleys-qc-pipeline/raw/2.2.3/workflow/envs/ashleys_base.yaml +# prefix: /conda-envs/87c04f5d115eff742eca84455513deba +# name: ashleys_base +# channels: +# - conda-forge +# - bioconda +# dependencies: +# - samtools +# - tabix +# - bwa +# - sambamba +# - mosaicatcher +# # - alfred +# - ashleys-qc +# - pandas +# # PUBLISHDIR +# - rsync +# # MULTIQC +# - multiqc +# # Fix sklearn update +# - scikit-learn=1.2.2 +RUN mkdir -p /conda-envs/87c04f5d115eff742eca84455513deba +ADD https://github.com/friendsofstrandseq/ashleys-qc-pipeline/raw/2.2.3/workflow/envs/ashleys_base.yaml /conda-envs/87c04f5d115eff742eca84455513deba/environment.yaml + +# Conda environment: +# source: https://github.com/friendsofstrandseq/ashleys-qc-pipeline/raw/2.2.3/workflow/envs/ashleys_rtools.yaml +# prefix: /conda-envs/9b847fc31baae8e01dfb7ce438a56b71 +# name: rtools +# channels: +# - conda-forge +# - bioconda +# - r +# - anaconda +# dependencies: +# # - bioconductor-biocparallel +# # - bioconductor-bsgenome +# # - bioconductor-bsgenome.hsapiens.ucsc.hg19 +# # - bioconductor-bsgenome.hsapiens.ucsc.hg38 +# # - bioconductor-fastseg +# # - bioconductor-genomicalignments +# - bioconductor-genomicranges +# # - bioconductor-rsamtools +# # - bioconductor-s4vectors +# - r-assertthat +# - r-base +# # - r-biocmanager +# - r-cowplot +# - r-data.table +# # - r-devtools +# # - r-doparallel +# # - r-foreach +# - r-ggplot2 +# # - r-gtools +# - r-reshape2 +# # - r-zoo +# # - r-dplyr +# # - r-mc2d +# # - r-pheatmap +# # - bioconductor-complexheatmap +# # - r-gplots +# - r-scales +# - r-rcolorbrewer +# # - r-stringr +# - r-cairo +# - fonts-anaconda +# # NEW +# - bioconductor-edger +# - r-r.utils +# # PLATE PLOT +# - r-dplyr +# - r-platetools +# - r-viridis +# # GC_correction +# - r-tidyr +# - r-ggpubr +# # SOLVE R lib issue +# - r-stringi=1.7.12 +RUN mkdir -p /conda-envs/9b847fc31baae8e01dfb7ce438a56b71 +ADD https://github.com/friendsofstrandseq/ashleys-qc-pipeline/raw/2.2.3/workflow/envs/ashleys_rtools.yaml /conda-envs/9b847fc31baae8e01dfb7ce438a56b71/environment.yaml + +# Conda environment: +# source: https://github.com/snakemake/snakemake-wrappers/raw/v1.7.0/bio/bwa/index/environment.yaml +# prefix: /conda-envs/5681728a49bd83ceed09ba194330c858 +# channels: +# - bioconda +# - conda-forge +# - defaults +# dependencies: +# - bwa ==0.7.17 +RUN mkdir -p /conda-envs/5681728a49bd83ceed09ba194330c858 +ADD https://github.com/snakemake/snakemake-wrappers/raw/v1.7.0/bio/bwa/index/environment.yaml /conda-envs/5681728a49bd83ceed09ba194330c858/environment.yaml + +# Conda environment: +# source: https://github.com/snakemake/snakemake-wrappers/raw/v1.7.0/bio/fastqc/environment.yaml +# prefix: /conda-envs/08d4368302a4bdf7eda6b536495efe7d +# channels: +# - bioconda +# - conda-forge +# - defaults +# dependencies: +# - fastqc ==0.11.9 +RUN mkdir -p /conda-envs/08d4368302a4bdf7eda6b536495efe7d +ADD https://github.com/snakemake/snakemake-wrappers/raw/v1.7.0/bio/fastqc/environment.yaml /conda-envs/08d4368302a4bdf7eda6b536495efe7d/environment.yaml + +# Conda environment: +# source: workflow/envs/mc_base.yaml +# prefix: /conda-envs/c80307395eddf442c2fb6870f40d822b +# name: mc-base +# channels: +# - conda-forge +# - bioconda +# dependencies: +# - pandas +# - intervaltree +# - scipy +# - pysam +# - tqdm +# - perl +# - pypdf2 +# - parmap +# # NEW +# - pyyaml +# - seaborn +# - matplotlib +# # SOLVE se-pe detection +# - samtools +# # ArbiGent Hufsah deps +# - pytables +# - xopen +RUN mkdir -p /conda-envs/c80307395eddf442c2fb6870f40d822b +COPY workflow/envs/mc_base.yaml /conda-envs/c80307395eddf442c2fb6870f40d822b/environment.yaml + +# Conda environment: +# source: workflow/envs/mc_bioinfo_tools.yaml +# prefix: /conda-envs/f251d84cdc9f25d0e14b48e780261d66 +# name: mc-bioinfo-tools +# channels: +# - conda-forge +# - bioconda +# dependencies: +# - bcftools +# - freebayes +# - mosaicatcher +# - samtools +# - tabix +# - whatshap +RUN mkdir -p /conda-envs/f251d84cdc9f25d0e14b48e780261d66 +COPY workflow/envs/mc_bioinfo_tools.yaml /conda-envs/f251d84cdc9f25d0e14b48e780261d66/environment.yaml + +# Conda environment: +# source: workflow/envs/rtools.yaml +# prefix: /conda-envs/598c87b6c764d05e0c66953cc67f2931 +# name: rtools +# channels: +# - bioconda +# - conda-forge +# - r +# - anaconda +# dependencies: +# # # NEW +# - strandphaser +# # ############### +# - bioconductor-biocparallel +# - bioconductor-bsgenome +# - bioconductor-bsgenome.hsapiens.ucsc.hg38 +# - bioconductor-complexheatmap +# # - bioconductor-fastseg +# - bioconductor-genomicalignments +# - bioconductor-genomicranges +# - bioconductor-rsamtools +# # - bioconductor-s4vectors +# - fonts-anaconda +# - r-assertthat +# - r-base +# - r-biocmanager +# - r-cairo +# - r-cowplot +# - r-data.table +# - r-devtools +# - r-doparallel +# - r-dplyr +# - r-foreach +# - r-ggplot2 +# - r-gplots +# - r-gtools +# - r-mc2d +# - r-rcolorbrewer +# - r-reshape2 +# - r-scales +# - r-stringr +# # SV_CALLS_DEV +# # - r-zoo +# - r-r.utils +# - r-ggnewscale +# # HEATMAP +# - r-tidyr +# # ARBIGENT +# - r-reshape +# - r-optparse +# - r-tidyr +# - r-ggbeeswarm +# - r-pheatmap +# # GC_correction +# - r-ggpubr +# - bioconductor-edger +# # SOLVE R lib issue +# - r-stringi=1.7.12 +RUN mkdir -p /conda-envs/598c87b6c764d05e0c66953cc67f2931 +COPY workflow/envs/rtools.yaml /conda-envs/598c87b6c764d05e0c66953cc67f2931/environment.yaml + +# Conda environment: +# source: workflow/envs/scNOVA/scNOVA_DL.yaml +# prefix: /conda-envs/1ede379ce8d378df7dca25b2bf4111f3 +# name: scNOVA_DL +# channels: +# - conda-forge +# - anaconda +# dependencies: +# - tensorflow=1.15.0 +# - scikit-learn=0.21.3 +# - python=3.7.4 +# - matplotlib=3.1.1 +# - pandas=0.25.3 +# - h5py=2.10.0 +# - numpy +# # scNOVA archive +# - unzip +# # Fix +RUN mkdir -p /conda-envs/1ede379ce8d378df7dca25b2bf4111f3 +COPY workflow/envs/scNOVA/scNOVA_DL.yaml /conda-envs/1ede379ce8d378df7dca25b2bf4111f3/environment.yaml + +# Conda environment: +# source: workflow/envs/scNOVA/scNOVA_R.yaml +# prefix: /conda-envs/193f60d48796dd17eb847ea689b863a9 +# name: scNOVA +# channels: +# - bioconda +# - conda-forge +# - r +# dependencies: +# - bioconductor-deseq2=1.30.0 +# - r-matrixstats=0.58.0 +# - r-pheatmap=1.0.12 +# - r-gplots=3.1.1 +# - r-umap=0.2.7.0 +# - r-rtsne=0.15 +# - r-factoextra=1.0.7 +# - r-pracma=2.3.3 +# - bioconductor-chromvar=1.12.0 +# - r-nabor=0.5.0 +# - bioconductor-motifmatchr=1.12.0 +# - bioconductor-bsgenome.hsapiens.ucsc.hg38=1.4.3 +# - bioconductor-jaspar2016=1.18.0 +# - r-codetools=0.2_18 +# - r-fitdistrplus +# - r-doparallel +# - r-foreach +RUN mkdir -p /conda-envs/193f60d48796dd17eb847ea689b863a9 +COPY workflow/envs/scNOVA/scNOVA_R.yaml /conda-envs/193f60d48796dd17eb847ea689b863a9/environment.yaml + +# Conda environment: +# source: workflow/envs/scNOVA/scNOVA_bioinfo_tools.yaml +# prefix: /conda-envs/ca9641251a8cb0057003875ad776c49f +# name: scNOVA_bioinfo_tools +# channels: +# - conda-forge +# - bioconda +# - anaconda +# dependencies: +# - samtools +# - biobambam +# - bedtools +RUN mkdir -p /conda-envs/ca9641251a8cb0057003875ad776c49f +COPY workflow/envs/scNOVA/scNOVA_bioinfo_tools.yaml /conda-envs/ca9641251a8cb0057003875ad776c49f/environment.yaml + +# Step 2: Generate conda environments + +RUN mamba env create --prefix /conda-envs/87c04f5d115eff742eca84455513deba --file /conda-envs/87c04f5d115eff742eca84455513deba/environment.yaml && \ + mamba env create --prefix /conda-envs/9b847fc31baae8e01dfb7ce438a56b71 --file /conda-envs/9b847fc31baae8e01dfb7ce438a56b71/environment.yaml && \ + mamba env create --prefix /conda-envs/5681728a49bd83ceed09ba194330c858 --file /conda-envs/5681728a49bd83ceed09ba194330c858/environment.yaml && \ + 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/598c87b6c764d05e0c66953cc67f2931 --file /conda-envs/598c87b6c764d05e0c66953cc67f2931/environment.yaml && \ + mamba env create --prefix /conda-envs/1ede379ce8d378df7dca25b2bf4111f3 --file /conda-envs/1ede379ce8d378df7dca25b2bf4111f3/environment.yaml && \ + mamba env create --prefix /conda-envs/193f60d48796dd17eb847ea689b863a9 --file /conda-envs/193f60d48796dd17eb847ea689b863a9/environment.yaml && \ + mamba env create --prefix /conda-envs/ca9641251a8cb0057003875ad776c49f --file /conda-envs/ca9641251a8cb0057003875ad776c49f/environment.yaml && \ + mamba clean --all -y + +# CUSTOM PART +RUN wget https://zenodo.org/record/7697400/files/BSgenome.T2T.CHM13.V2_1.0.0.tar.gz -P /workflow/data/ref_genomes/ +COPY /workflow/scripts/utils/install_R_package.R /conda-envs/ +RUN chmod -R 0777 /conda-envs/598c87b6c764d05e0c66953cc67f2931/lib/R/library && /conda-envs/598c87b6c764d05e0c66953cc67f2931/bin/Rscript /conda-envs/install_R_package.R /workflow/data/ref_genomes/BSgenome.T2T.CHM13.V2_1.0.0.tar.gz diff --git a/github-actions-runner/add_T2T_part_to_Dockerfile.sh b/github-actions-runner/add_T2T_part_to_Dockerfile.sh index 7c631edd..3d7fcc85 100644 --- a/github-actions-runner/add_T2T_part_to_Dockerfile.sh +++ b/github-actions-runner/add_T2T_part_to_Dockerfile.sh @@ -25,7 +25,6 @@ fi # Append custom steps to the Dockerfile { - echo '\n' echo "# CUSTOM PART" echo "RUN wget https://zenodo.org/record/7697400/files/BSgenome.T2T.CHM13.V2_1.0.0.tar.gz -P /workflow/data/ref_genomes/" echo "COPY /workflow/scripts/utils/install_R_package.R /conda-envs/"