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@weber8thomas
weber8thomas committed Dec 5, 2023
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300 changes: 300 additions & 0 deletions github-actions-runner/Dockerfile-2.2.4.dockerfile
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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
1 change: 0 additions & 1 deletion github-actions-runner/add_T2T_part_to_Dockerfile.sh
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# 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/"
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