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Dockerfile
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FROM condaforge/mambaforge:latest
LABEL io.github.snakemake.containerized="true"
LABEL io.github.snakemake.conda_env_hash="59e93cf8f17044dd4c67a8f4249f98cb59359406b22460eaee3da067704d29e3"
# Step 1: Retrieve conda environments
# Conda environment:
# source: https://github.com/snakemake/snakemake-wrappers/raw/v1.26.0/bio/bwa/index/environment.yaml
# prefix: /conda-envs/c2273db56372af81b557728cddb6ccd7
# channels:
# - conda-forge
# - bioconda
# - nodefaults
# dependencies:
# - bwa =0.7.17
RUN mkdir -p /conda-envs/c2273db56372af81b557728cddb6ccd7
ADD https://github.com/snakemake/snakemake-wrappers/raw/v1.26.0/bio/bwa/index/environment.yaml /conda-envs/c2273db56372af81b557728cddb6ccd7/environment.yaml
# Conda environment:
# source: https://github.com/snakemake/snakemake-wrappers/raw/v1.26.0/bio/star/index/environment.yaml
# prefix: /conda-envs/62ead550e24a99a2d873f1fc4ab2e9d3
# channels:
# - conda-forge
# - bioconda
# - nodefaults
# dependencies:
# - star =2.7.10b
RUN mkdir -p /conda-envs/62ead550e24a99a2d873f1fc4ab2e9d3
ADD https://github.com/snakemake/snakemake-wrappers/raw/v1.26.0/bio/star/index/environment.yaml /conda-envs/62ead550e24a99a2d873f1fc4ab2e9d3/environment.yaml
# Conda environment:
# source: https://github.com/snakemake/snakemake-wrappers/raw/v1.28.0/bio/samtools/faidx/environment.yaml
# prefix: /conda-envs/f49ecd58ca2f64505be52944e62793eb
# channels:
# - conda-forge
# - bioconda
# - nodefaults
# dependencies:
# - samtools =1.17
# - snakemake-wrapper-utils =0.5.3
RUN mkdir -p /conda-envs/f49ecd58ca2f64505be52944e62793eb
ADD https://github.com/snakemake/snakemake-wrappers/raw/v1.28.0/bio/samtools/faidx/environment.yaml /conda-envs/f49ecd58ca2f64505be52944e62793eb/environment.yaml
# Conda environment:
# source: https://github.com/snakemake/snakemake-wrappers/raw/v1.31.1/bio/vep/annotate/environment.yaml
# prefix: /conda-envs/fc332fe00ffc9fb8703741177c361800
# channels:
# - conda-forge
# - bioconda
# - nodefaults
# dependencies:
# - ensembl-vep =109.3
# - bcftools =1.16
# - perl-encode-locale =1.05
# - perl =5.32.1
RUN mkdir -p /conda-envs/fc332fe00ffc9fb8703741177c361800
ADD https://github.com/snakemake/snakemake-wrappers/raw/v1.31.1/bio/vep/annotate/environment.yaml /conda-envs/fc332fe00ffc9fb8703741177c361800/environment.yaml
# Conda environment:
# source: https://github.com/snakemake/snakemake-wrappers/raw/v1.31.1/bio/vep/plugins/environment.yaml
# prefix: /conda-envs/b823871fbdb958824831a5d19ef346f7
# channels:
# - conda-forge
# - nodefaults
# dependencies:
# - python =3.11.3
RUN mkdir -p /conda-envs/b823871fbdb958824831a5d19ef346f7
ADD https://github.com/snakemake/snakemake-wrappers/raw/v1.31.1/bio/vep/plugins/environment.yaml /conda-envs/b823871fbdb958824831a5d19ef346f7/environment.yaml
# Conda environment:
# source: https://github.com/snakemake/snakemake-wrappers/raw/v2.2.1/bio/fastp/environment.yaml
# prefix: /conda-envs/371fd38cc0bae1ae0eff1fdbcd1fb191
# channels:
# - conda-forge
# - bioconda
# - nodefaults
# dependencies:
# - fastp =0.23.4
RUN mkdir -p /conda-envs/371fd38cc0bae1ae0eff1fdbcd1fb191
ADD https://github.com/snakemake/snakemake-wrappers/raw/v2.2.1/bio/fastp/environment.yaml /conda-envs/371fd38cc0bae1ae0eff1fdbcd1fb191/environment.yaml
# Conda environment:
# source: https://github.com/snakemake/snakemake-wrappers/raw/v2.2.1/bio/fastqc/environment.yaml
# prefix: /conda-envs/4c5e83029c4c995ec347593201305c58
# channels:
# - conda-forge
# - bioconda
# - nodefaults
# dependencies:
# - fastqc =0.12.1
# - snakemake-wrapper-utils =0.5.3
RUN mkdir -p /conda-envs/4c5e83029c4c995ec347593201305c58
ADD https://github.com/snakemake/snakemake-wrappers/raw/v2.2.1/bio/fastqc/environment.yaml /conda-envs/4c5e83029c4c995ec347593201305c58/environment.yaml
# Conda environment:
# source: https://github.com/snakemake/snakemake-wrappers/raw/v2.3.0/bio/samtools/index/environment.yaml
# prefix: /conda-envs/07acb90021639eb8e01afad917437175
# channels:
# - conda-forge
# - bioconda
# - nodefaults
# dependencies:
# - samtools =1.17
RUN mkdir -p /conda-envs/07acb90021639eb8e01afad917437175
ADD https://github.com/snakemake/snakemake-wrappers/raw/v2.3.0/bio/samtools/index/environment.yaml /conda-envs/07acb90021639eb8e01afad917437175/environment.yaml
# Conda environment:
# source: workflow/envs/basic.yml
# prefix: /conda-envs/433868d00d0dc4be52f375e4825c470c
# channels:
# - conda-forge
# - bioconda
# dependencies:
# - python=3.8
# - bwa=0.7.17
# - samtools=1.16.1
RUN mkdir -p /conda-envs/433868d00d0dc4be52f375e4825c470c
COPY workflow/envs/basic.yml /conda-envs/433868d00d0dc4be52f375e4825c470c/environment.yaml
# Conda environment:
# source: workflow/envs/manipulate_vcf.yml
# prefix: /conda-envs/6eaaf5e74784e6f8c26fdcd742e36151
# channels:
# - bioconda
# - conda-forge
# - defaults
# dependencies:
# - pip=23.1.2
# - pip:
# - vcfpy==0.13.6
# - intervaltree==3.1.0
RUN mkdir -p /conda-envs/6eaaf5e74784e6f8c26fdcd742e36151
COPY workflow/envs/manipulate_vcf.yml /conda-envs/6eaaf5e74784e6f8c26fdcd742e36151/environment.yaml
# Conda environment:
# source: workflow/envs/optitype.yml
# prefix: /conda-envs/fb6854ad4d0c4f83583dc02e8514c04a
# channels:
# - conda-forge
# - bioconda
# - nodefaults
# dependencies:
# - optitype =1.3.5
# - pysam
RUN mkdir -p /conda-envs/fb6854ad4d0c4f83583dc02e8514c04a
COPY workflow/envs/optitype.yml /conda-envs/fb6854ad4d0c4f83583dc02e8514c04a/environment.yaml
# Conda environment:
# source: workflow/envs/priorization.yml
# prefix: /conda-envs/68a7987b5f06060b54044245991e2e18
# channels:
# - bioconda
# - conda-forge
# dependencies:
# - python>=3.6
# - vcfpy
# - pyfaidx
# - configargparse
RUN mkdir -p /conda-envs/68a7987b5f06060b54044245991e2e18
COPY workflow/envs/priorization.yml /conda-envs/68a7987b5f06060b54044245991e2e18/environment.yaml
# Conda environment:
# source: workflow/envs/samtools.yml
# prefix: /conda-envs/73c25277031fb2557ef8f6ce52038e12
# channels:
# - bioconda
# dependencies:
# - samtools
# - bcftools
RUN mkdir -p /conda-envs/73c25277031fb2557ef8f6ce52038e12
COPY workflow/envs/samtools.yml /conda-envs/73c25277031fb2557ef8f6ce52038e12/environment.yaml
# Conda environment:
# source: workflow/envs/transindel.yml
# prefix: /conda-envs/1f213f31e028357cabefb1af5246e324
# channels:
# - bioconda
# - conda-forge
# - defaults
# - r
# dependencies:
# - samtools
# - pysam
# - htseq
# - pyfaidx
# - pip
# - pip:
# - vcfpy==0.13.6
RUN mkdir -p /conda-envs/1f213f31e028357cabefb1af5246e324
COPY workflow/envs/transindel.yml /conda-envs/1f213f31e028357cabefb1af5246e324/environment.yaml
# Conda environment:
# source: workflow/envs/yara.yml
# prefix: /conda-envs/b92240a0a4d42d7bd8bbe57c8f338de6
# channels:
# - bioconda
# dependencies:
# - yara
# - samtools
RUN mkdir -p /conda-envs/b92240a0a4d42d7bd8bbe57c8f338de6
COPY workflow/envs/yara.yml /conda-envs/b92240a0a4d42d7bd8bbe57c8f338de6/environment.yaml
# Step 2: Generate conda environments
RUN mamba env create --prefix /conda-envs/c2273db56372af81b557728cddb6ccd7 --file /conda-envs/c2273db56372af81b557728cddb6ccd7/environment.yaml && \
mamba env create --prefix /conda-envs/62ead550e24a99a2d873f1fc4ab2e9d3 --file /conda-envs/62ead550e24a99a2d873f1fc4ab2e9d3/environment.yaml && \
mamba env create --prefix /conda-envs/f49ecd58ca2f64505be52944e62793eb --file /conda-envs/f49ecd58ca2f64505be52944e62793eb/environment.yaml && \
mamba env create --prefix /conda-envs/fc332fe00ffc9fb8703741177c361800 --file /conda-envs/fc332fe00ffc9fb8703741177c361800/environment.yaml && \
mamba env create --prefix /conda-envs/b823871fbdb958824831a5d19ef346f7 --file /conda-envs/b823871fbdb958824831a5d19ef346f7/environment.yaml && \
mamba env create --prefix /conda-envs/371fd38cc0bae1ae0eff1fdbcd1fb191 --file /conda-envs/371fd38cc0bae1ae0eff1fdbcd1fb191/environment.yaml && \
mamba env create --prefix /conda-envs/4c5e83029c4c995ec347593201305c58 --file /conda-envs/4c5e83029c4c995ec347593201305c58/environment.yaml && \
mamba env create --prefix /conda-envs/07acb90021639eb8e01afad917437175 --file /conda-envs/07acb90021639eb8e01afad917437175/environment.yaml && \
mamba env create --prefix /conda-envs/433868d00d0dc4be52f375e4825c470c --file /conda-envs/433868d00d0dc4be52f375e4825c470c/environment.yaml && \
mamba env create --prefix /conda-envs/6eaaf5e74784e6f8c26fdcd742e36151 --file /conda-envs/6eaaf5e74784e6f8c26fdcd742e36151/environment.yaml && \
mamba env create --prefix /conda-envs/fb6854ad4d0c4f83583dc02e8514c04a --file /conda-envs/fb6854ad4d0c4f83583dc02e8514c04a/environment.yaml && \
mamba env create --prefix /conda-envs/68a7987b5f06060b54044245991e2e18 --file /conda-envs/68a7987b5f06060b54044245991e2e18/environment.yaml && \
mamba env create --prefix /conda-envs/73c25277031fb2557ef8f6ce52038e12 --file /conda-envs/73c25277031fb2557ef8f6ce52038e12/environment.yaml && \
mamba env create --prefix /conda-envs/1f213f31e028357cabefb1af5246e324 --file /conda-envs/1f213f31e028357cabefb1af5246e324/environment.yaml && \
mamba env create --prefix /conda-envs/b92240a0a4d42d7bd8bbe57c8f338de6 --file /conda-envs/b92240a0a4d42d7bd8bbe57c8f338de6/environment.yaml && \
mamba clean --all -y