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‎.docker/README.md

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# Dockerfiles for each version (>= v0.5.0)
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This directory contains Dockerfiles associated with each release.
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The Docker image derived from this file contains all Conda environments for each rule, i.e. the whole workflow is run in one image.
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These images are shared via [Docker Hub](https://hub.docker.com/repository/docker/niekwit/damid-seq/general) and are generated as follows (from directory with workflow code):
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```shell
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$ snakemake --containerize > Dockerfile
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$ sudo docker build -t niekwit/damid-seq:{VERSION} .
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$ sudo docker login
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$ sudo docker push niekwit/damid-seq:{VERSION}
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```

‎.docker/v0.5.0/Dockerfile

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FROM condaforge/mambaforge:latest
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LABEL io.github.snakemake.containerized="true"
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LABEL io.github.snakemake.conda_env_hash="c5a326651c7f183cccd58d1723ac96357a3ce6654daf36293784636da3a119f2"
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# Step 1: Retrieve conda environments
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# Conda environment:
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# source: https://github.com/snakemake/snakemake-wrappers/raw/v3.10.2/bio/bowtie2/build/environment.yaml
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# prefix: /conda-envs/e471b5222afe25a895718be01070f68f
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# channels:
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# - conda-forge
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# - bioconda
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# - nodefaults
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# dependencies:
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# - bowtie2 =2.5.3
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RUN mkdir -p /conda-envs/e471b5222afe25a895718be01070f68f
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ADD https://github.com/snakemake/snakemake-wrappers/raw/v3.10.2/bio/bowtie2/build/environment.yaml /conda-envs/e471b5222afe25a895718be01070f68f/environment.yaml
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# Conda environment:
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# source: https://github.com/snakemake/snakemake-wrappers/raw/v3.10.2/bio/fastqc/environment.yaml
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# prefix: /conda-envs/90ea9a0a5f4de478eb6aa43932774175
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# channels:
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# - conda-forge
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# - bioconda
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# - nodefaults
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# dependencies:
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# - fastqc =0.12.1
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# - snakemake-wrapper-utils =0.6.2
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RUN mkdir -p /conda-envs/90ea9a0a5f4de478eb6aa43932774175
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ADD https://github.com/snakemake/snakemake-wrappers/raw/v3.10.2/bio/fastqc/environment.yaml /conda-envs/90ea9a0a5f4de478eb6aa43932774175/environment.yaml
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# Conda environment:
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# source: https://github.com/snakemake/snakemake-wrappers/raw/v3.10.2/bio/samtools/faidx/environment.yaml
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# prefix: /conda-envs/b29db9b4576aa24f6ca5cdabda9911b4
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# channels:
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# - conda-forge
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# - bioconda
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# - nodefaults
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# dependencies:
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# - samtools =1.20
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# - snakemake-wrapper-utils =0.6.2
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RUN mkdir -p /conda-envs/b29db9b4576aa24f6ca5cdabda9911b4
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ADD https://github.com/snakemake/snakemake-wrappers/raw/v3.10.2/bio/samtools/faidx/environment.yaml /conda-envs/b29db9b4576aa24f6ca5cdabda9911b4/environment.yaml
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# Conda environment:
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# source: https://github.com/snakemake/snakemake-wrappers/raw/v3.10.2/bio/samtools/index/environment.yaml
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# prefix: /conda-envs/adec7d399fa9492178d9caa96f93852d
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# channels:
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# - conda-forge
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# - bioconda
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# - nodefaults
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# dependencies:
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# - samtools =1.20
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RUN mkdir -p /conda-envs/adec7d399fa9492178d9caa96f93852d
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ADD https://github.com/snakemake/snakemake-wrappers/raw/v3.10.2/bio/samtools/index/environment.yaml /conda-envs/adec7d399fa9492178d9caa96f93852d/environment.yaml
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# Conda environment:
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# source: workflow/envs/R.yaml
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# prefix: /conda-envs/b287d5a87a7b181ed59611ddc5af0a8f
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# name: R
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# channels:
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# - conda-forge
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# - bioconda
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# - defaults
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# dependencies:
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# - r-base=4.3
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# - r-tidyverse=2.0.0
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# - r-cowplot=1.1.2
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# - r-reshape2=1.4.4
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# - r-rcolorbrewer=1.1_3
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# - r-ggrepel=0.9.4
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# - r-scales=1.3.0
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# - bioconductor-chipseeker=1.38.0
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# - bioconductor-genomicfeatures=1.54.1
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# - bioconductor-rtracklayer=1.62.0
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# - r-viridislite=0.4.2
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RUN mkdir -p /conda-envs/b287d5a87a7b181ed59611ddc5af0a8f
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COPY workflow/envs/R.yaml /conda-envs/b287d5a87a7b181ed59611ddc5af0a8f/environment.yaml
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# Conda environment:
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# source: workflow/envs/damid.yaml
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# prefix: /conda-envs/cb2a9c9685efe98f401d666d5b884a76
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# name: damid
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# channels:
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# - conda-forge
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# - bioconda
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# - defaults
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# dependencies:
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# - pigz=2.8
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# - samtools=1.19
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# - bowtie2=2.5.3
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# - perl=5.32.1
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# - perl-inline-c=0.81
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# - r-base=4.3.2
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# - igvtools=2.16.2
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# - pandas=2.2.0
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# - pyarrow=14.0.2 #pandas dependency, somehow not in pandas recipe
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RUN mkdir -p /conda-envs/cb2a9c9685efe98f401d666d5b884a76
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COPY workflow/envs/damid.yaml /conda-envs/cb2a9c9685efe98f401d666d5b884a76/environment.yaml
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# Conda environment:
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# source: workflow/envs/deeptools.yaml
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# prefix: /conda-envs/0c5edaf30d052120fe12000c137275cb
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# name: deeptools
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# channels:
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# - conda-forge
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# - bioconda
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# - defaults
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# dependencies:
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# - deeptools=3.5.4
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# - python=3.10
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# - ucsc-bedgraphtobigwig=445
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# - wiggletools=1.2.11
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# - ucsc-wigtobigwig=447
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RUN mkdir -p /conda-envs/0c5edaf30d052120fe12000c137275cb
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COPY workflow/envs/deeptools.yaml /conda-envs/0c5edaf30d052120fe12000c137275cb/environment.yaml
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# Conda environment:
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# source: workflow/envs/peak_calling.yaml
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# prefix: /conda-envs/35dbd4f499c2bf378ca66a63855a13dc
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# name: peak_calling
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# channels:
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# - conda-forge
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# - bioconda
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# - defaults
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# dependencies:
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# - python=3.9
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# - pandas=2.1.4
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# - bedtools=2.31.1
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# - bedops=2.4.41
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# - biopython=1.78
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# - macs2=2.2.9.1
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RUN mkdir -p /conda-envs/35dbd4f499c2bf378ca66a63855a13dc
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COPY workflow/envs/peak_calling.yaml /conda-envs/35dbd4f499c2bf378ca66a63855a13dc/environment.yaml
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# Conda environment:
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# source: workflow/envs/trim.yaml
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# prefix: /conda-envs/eb3add28986aad43900ea2d897797774
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# name: trim
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# channels:
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# - conda-forge
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# - bioconda
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# - defaults
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# dependencies:
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# - python=3.10
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# - trim-galore=0.6.10
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# - multiqc=1.19
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RUN mkdir -p /conda-envs/eb3add28986aad43900ea2d897797774
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COPY workflow/envs/trim.yaml /conda-envs/eb3add28986aad43900ea2d897797774/environment.yaml
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# Step 2: Generate conda environments
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RUN mamba env create --prefix /conda-envs/e471b5222afe25a895718be01070f68f --file /conda-envs/e471b5222afe25a895718be01070f68f/environment.yaml && \
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mamba env create --prefix /conda-envs/90ea9a0a5f4de478eb6aa43932774175 --file /conda-envs/90ea9a0a5f4de478eb6aa43932774175/environment.yaml && \
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mamba env create --prefix /conda-envs/b29db9b4576aa24f6ca5cdabda9911b4 --file /conda-envs/b29db9b4576aa24f6ca5cdabda9911b4/environment.yaml && \
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mamba env create --prefix /conda-envs/adec7d399fa9492178d9caa96f93852d --file /conda-envs/adec7d399fa9492178d9caa96f93852d/environment.yaml && \
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mamba env create --prefix /conda-envs/b287d5a87a7b181ed59611ddc5af0a8f --file /conda-envs/b287d5a87a7b181ed59611ddc5af0a8f/environment.yaml && \
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mamba env create --prefix /conda-envs/cb2a9c9685efe98f401d666d5b884a76 --file /conda-envs/cb2a9c9685efe98f401d666d5b884a76/environment.yaml && \
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mamba env create --prefix /conda-envs/0c5edaf30d052120fe12000c137275cb --file /conda-envs/0c5edaf30d052120fe12000c137275cb/environment.yaml && \
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mamba env create --prefix /conda-envs/35dbd4f499c2bf378ca66a63855a13dc --file /conda-envs/35dbd4f499c2bf378ca66a63855a13dc/environment.yaml && \
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mamba env create --prefix /conda-envs/eb3add28986aad43900ea2d897797774 --file /conda-envs/eb3add28986aad43900ea2d897797774/environment.yaml && \
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mamba clean --all -y

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