Containerized.yaml

FROM condaforge/mambaforge:latest
LABEL io.github.snakemake.containerized="true"
LABEL io.github.snakemake.conda_env_hash="5bc8ff0455fe0665bf3e263dd1f199b62fb7667eb7cba687564d66faa0c8a576"

# Step 1: Retrieve conda environments

# Conda environment:
#   source: envs/biopythonworkbench.yaml
#   prefix: /conda-envs/dd35d0924e74f8ddd08ab182fd45fb7a
#   name: BioPythonWorkbench
#   
#   channels:
#     - conda-forge
#     - bioconda
#   
#   dependencies:
#     - biopython=1.78
#     - python=3.7
#     - regex
#     - openssl = 1.0
#     - samtools = 1.9
#     - seaborn = 0.9.0
#     - scipy = 1.2.1
#     - pysam = 0.15.2
RUN mkdir -p /conda-envs/dd35d0924e74f8ddd08ab182fd45fb7a
COPY envs/biopythonworkbench.yaml /conda-envs/dd35d0924e74f8ddd08ab182fd45fb7a/environment.yaml

# Conda environment:
#   source: envs/bubblegun.yaml
#   prefix: /conda-envs/f41f5f010351dae40f5533ec40c5318c
#   name: bubblegun
#   channels:
#     - defaults
#   dependencies:
#     - pip:
#         - git+https://github.com/fawaz-dabbaghieh/bubble_gun.git@v1.1.0
RUN mkdir -p /conda-envs/f41f5f010351dae40f5533ec40c5318c
COPY envs/bubblegun.yaml /conda-envs/f41f5f010351dae40f5533ec40c5318c/environment.yaml

# Conda environment:
#   source: envs/fastp.yaml
#   prefix: /conda-envs/136a25abbd0e323b4374d8420a0d10a2
#   name: Fastp
#   
#   channels:
#     - conda-forge
#     - bioconda
#   
#   dependencies:
#     - fastp = 0.20.0
RUN mkdir -p /conda-envs/136a25abbd0e323b4374d8420a0d10a2
COPY envs/fastp.yaml /conda-envs/136a25abbd0e323b4374d8420a0d10a2/environment.yaml

# Conda environment:
#   source: envs/freebayes.yaml
#   prefix: /conda-envs/cb781f676fafdca20da354465b43ef17
#   name: FreeBayes
#   
#   channels:
#     - conda-forge
#     - bioconda
#   
#   dependencies:
#     - vcfpy = 0.12.1
#     - freebayes = 1.3.2
RUN mkdir -p /conda-envs/cb781f676fafdca20da354465b43ef17
COPY envs/freebayes.yaml /conda-envs/cb781f676fafdca20da354465b43ef17/environment.yaml

# Conda environment:
#   source: envs/graphaligner.yaml
#   prefix: /conda-envs/21cd67a1b5af5ed83c331dbe5ab3da98
#   name: GraphAligner
#   
#   channels:
#     - defaults
#     - bioconda
#     - conda-forge
#   
#   dependencies:
#     - graphaligner = 1.0.12
RUN mkdir -p /conda-envs/21cd67a1b5af5ed83c331dbe5ab3da98
COPY envs/graphaligner.yaml /conda-envs/21cd67a1b5af5ed83c331dbe5ab3da98/environment.yaml

# Conda environment:
#   source: envs/perl.yaml
#   prefix: /conda-envs/539abccfb55947617de4f6a9867b5a82
#   name: Perl
#   
#   channels:
#     - conda-forge
#     - bioconda
#   
#   dependencies:
#     - perl = 5.26.2
RUN mkdir -p /conda-envs/539abccfb55947617de4f6a9867b5a82
COPY envs/perl.yaml /conda-envs/539abccfb55947617de4f6a9867b5a82/environment.yaml

# Conda environment:
#   source: envs/realign.yaml
#   prefix: /conda-envs/6a51a8e6053d01010b475e9d4469c72f
#   name: realign
#   
#   channels:
#     - conda-forge
#     - bioconda
#   
#   dependencies:
#     - bwa = 0.7.17
#     - samtools = 1.10
#     - bcftools = 1.10.2
RUN mkdir -p /conda-envs/6a51a8e6053d01010b475e9d4469c72f
COPY envs/realign.yaml /conda-envs/6a51a8e6053d01010b475e9d4469c72f/environment.yaml

# Conda environment:
#   source: envs/snpEff.yaml
#   prefix: /conda-envs/09544774d13a78b52ccadc8d16ce3a7f
#   name: snpEff
#   
#   channels:
#     - conda-forge
#     - bioconda
#   
#   dependencies:
#     - snpEff = 5.0
RUN mkdir -p /conda-envs/09544774d13a78b52ccadc8d16ce3a7f
COPY envs/snpEff.yaml /conda-envs/09544774d13a78b52ccadc8d16ce3a7f/environment.yaml

# Conda environment:
#   source: envs/tabix.yaml
#   prefix: /conda-envs/7a3dde4bdb157c84c6f94fd4d5b1e145
#   name: Tabix
#   
#   channels:
#     - main
#     - bioconda
#   
#   dependencies:
#     - tabix = 0.2.6
RUN mkdir -p /conda-envs/7a3dde4bdb157c84c6f94fd4d5b1e145
COPY envs/tabix.yaml /conda-envs/7a3dde4bdb157c84c6f94fd4d5b1e145/environment.yaml

# Conda environment:
#   source: envs/vcfpy.yaml
#   prefix: /conda-envs/ccbf4f98fbf836ecfedbe13ce212ef0e
#   name: vcfpy
#   
#   channels:
#     - conda-forge
#     - bioconda
#   
#   dependencies:
#     - vcfpy = 0.13
#     - scipy = 1.2.1
#     - biopython = 1.71
#     - pip:
#       - upsetplot == 0.4.1
#       - pandas == 1.1.3
RUN mkdir -p /conda-envs/ccbf4f98fbf836ecfedbe13ce212ef0e
COPY envs/vcfpy.yaml /conda-envs/ccbf4f98fbf836ecfedbe13ce212ef0e/environment.yaml

# Conda environment:
#   source: envs/vg.yaml
#   prefix: /conda-envs/01c584e0f11dd76facd4aaec0e5fbb34
#   name: vg
#   
#   channels:
#     - conda-forge
#     - bioconda
#   
#   dependencies:
#     - vg = 1.24
RUN mkdir -p /conda-envs/01c584e0f11dd76facd4aaec0e5fbb34
COPY envs/vg.yaml /conda-envs/01c584e0f11dd76facd4aaec0e5fbb34/environment.yaml

# Conda environment:
#   source: envs/vt.yaml
#   prefix: /conda-envs/abc940c44070c41f466b8a2821b4e242
#   name: vt
#   
#   channels:
#     - conda-forge
#     - bioconda
#   
#   dependencies:
#     - vt=2015.11.10=he941832_3
RUN mkdir -p /conda-envs/abc940c44070c41f466b8a2821b4e242
COPY envs/vt.yaml /conda-envs/abc940c44070c41f466b8a2821b4e242/environment.yaml

# Step 2: Generate conda environments

RUN mamba env create --prefix /conda-envs/dd35d0924e74f8ddd08ab182fd45fb7a --file /conda-envs/dd35d0924e74f8ddd08ab182fd45fb7a/environment.yaml && \
    mamba env create --prefix /conda-envs/f41f5f010351dae40f5533ec40c5318c --file /conda-envs/f41f5f010351dae40f5533ec40c5318c/environment.yaml && \
    mamba env create --prefix /conda-envs/136a25abbd0e323b4374d8420a0d10a2 --file /conda-envs/136a25abbd0e323b4374d8420a0d10a2/environment.yaml && \
    mamba env create --prefix /conda-envs/cb781f676fafdca20da354465b43ef17 --file /conda-envs/cb781f676fafdca20da354465b43ef17/environment.yaml && \
    mamba env create --prefix /conda-envs/21cd67a1b5af5ed83c331dbe5ab3da98 --file /conda-envs/21cd67a1b5af5ed83c331dbe5ab3da98/environment.yaml && \
    mamba env create --prefix /conda-envs/539abccfb55947617de4f6a9867b5a82 --file /conda-envs/539abccfb55947617de4f6a9867b5a82/environment.yaml && \
    mamba env create --prefix /conda-envs/6a51a8e6053d01010b475e9d4469c72f --file /conda-envs/6a51a8e6053d01010b475e9d4469c72f/environment.yaml && \
    mamba env create --prefix /conda-envs/09544774d13a78b52ccadc8d16ce3a7f --file /conda-envs/09544774d13a78b52ccadc8d16ce3a7f/environment.yaml && \
    mamba env create --prefix /conda-envs/7a3dde4bdb157c84c6f94fd4d5b1e145 --file /conda-envs/7a3dde4bdb157c84c6f94fd4d5b1e145/environment.yaml && \
    mamba env create --prefix /conda-envs/ccbf4f98fbf836ecfedbe13ce212ef0e --file /conda-envs/ccbf4f98fbf836ecfedbe13ce212ef0e/environment.yaml && \
    mamba env create --prefix /conda-envs/01c584e0f11dd76facd4aaec0e5fbb34 --file /conda-envs/01c584e0f11dd76facd4aaec0e5fbb34/environment.yaml && \
    mamba env create --prefix /conda-envs/abc940c44070c41f466b8a2821b4e242 --file /conda-envs/abc940c44070c41f466b8a2821b4e242/environment.yaml && \
    mamba clean --all -y