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Dockerfile
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ARG VERSION=0.2.0
FROM condaforge/miniforge3:latest
LABEL io.github.snakemake.containerized="true"
LABEL io.github.snakemake.conda_env_hash="7a57714fe74eb25255d53b45e2095cd8a4dd4fe73db79006353670c432af97b1"
# Step 1: Retrieve conda environments
# Conda environment:
# source: workflow/envs/NGmerge.yaml
# prefix: /conda-envs/8b5bbd33d7ccdbbe3a28773771abe2b3
# ---
# channels:
# - conda-forge
# - bioconda
# dependencies:
# - ngmerge=0.3
# - python
# - click
# - htslib
RUN mkdir -p /conda-envs/8b5bbd33d7ccdbbe3a28773771abe2b3
COPY workflow/envs/NGmerge.yaml /conda-envs/8b5bbd33d7ccdbbe3a28773771abe2b3/environment.yaml
# Conda environment:
# source: workflow/envs/bbmap_samtools_htslib.yaml
# prefix: /conda-envs/f24b0ccfc23aadb93b466380cd592733
# ---
# channels:
# - bioconda
# - conda-forge
# dependencies:
# - bbmap
# - samtools
# - htslib
RUN mkdir -p /conda-envs/f24b0ccfc23aadb93b466380cd592733
COPY workflow/envs/bbmap_samtools_htslib.yaml /conda-envs/f24b0ccfc23aadb93b466380cd592733/environment.yaml
# Conda environment:
# source: workflow/envs/bwa_samtools_picard_htslib.yaml
# prefix: /conda-envs/a0a27bbdca540d02023c7fdcf819bfc1
# ---
# channels:
# - bioconda
# - conda-forge
# dependencies:
# - bwa
# - samtools
# - picard
# - htslib
RUN mkdir -p /conda-envs/a0a27bbdca540d02023c7fdcf819bfc1
COPY workflow/envs/bwa_samtools_picard_htslib.yaml /conda-envs/a0a27bbdca540d02023c7fdcf819bfc1/environment.yaml
# Conda environment:
# source: workflow/envs/default.yaml
# prefix: /conda-envs/899c0a8c04c6edeed4b242dbc3e0e1c8
# ---
# channels:
# - conda-forge
# - bioconda
# dependencies:
# - htslib
RUN mkdir -p /conda-envs/899c0a8c04c6edeed4b242dbc3e0e1c8
COPY workflow/envs/default.yaml /conda-envs/899c0a8c04c6edeed4b242dbc3e0e1c8/environment.yaml
# Conda environment:
# source: workflow/envs/fastqsplitter.yaml
# prefix: /conda-envs/e5aec3a0d6b8921994e5305d4f89e90f
# ---
# channels:
# - bioconda
# - conda-forge
# dependencies:
# - fastqsplitter
RUN mkdir -p /conda-envs/e5aec3a0d6b8921994e5305d4f89e90f
COPY workflow/envs/fastqsplitter.yaml /conda-envs/e5aec3a0d6b8921994e5305d4f89e90f/environment.yaml
# Conda environment:
# source: workflow/envs/python3.yaml
# prefix: /conda-envs/a4e1b935cbca52df9b6f192ff86c464c
# ---
# channels:
# - conda-forge
# - bioconda
# dependencies:
# - biopython
# - click
# - dask
# - matplotlib
# - numpy
# - pandas
# - python
# - pysam
# - pyfastx
RUN mkdir -p /conda-envs/a4e1b935cbca52df9b6f192ff86c464c
COPY workflow/envs/python3.yaml /conda-envs/a4e1b935cbca52df9b6f192ff86c464c/environment.yaml
# Conda environment:
# source: workflow/envs/r.yaml
# prefix: /conda-envs/ae3e37bf43cbb30416a885168e10c552
# ---
# channels:
# - conda-forge
# - bioconda
# dependencies:
# - r-base
# - r-cowplot
# - r-cairo
# - r-optparse
# - r-tidyverse
RUN mkdir -p /conda-envs/ae3e37bf43cbb30416a885168e10c552
COPY workflow/envs/r.yaml /conda-envs/ae3e37bf43cbb30416a885168e10c552/environment.yaml
# Conda environment:
# source: workflow/envs/python27.yaml
# prefix: /conda-envs/cb972f023533b03e742da9095ce03b06
# ---
# channels:
# - bioconda
# - conda-forge
# dependencies:
# - htslib
# - pysam
# - python=2.7
# - samtools
RUN mkdir -p /conda-envs/cb972f023533b03e742da9095ce03b06
COPY workflow/envs/python27.yaml /conda-envs/cb972f023533b03e742da9095ce03b06/environment.yaml
# Conda environment:
# source: workflow/envs/cutadapt.yaml
# prefix: /conda-envs/a3e2fce7f2f6fdbe1aa97232e3def601
# ---
# channels:
# - conda-forge
# - bioconda
# dependencies:
# - cutadapt
RUN mkdir -p /conda-envs/a3e2fce7f2f6fdbe1aa97232e3def601
COPY workflow/envs/cutadapt.yaml /conda-envs/a3e2fce7f2f6fdbe1aa97232e3def601/environment.yaml
# Conda environment:
# source: workflow/envs/quarto.yaml
# prefix: /conda-envs/b933cc1aa7c25db04635e7ec0e37f80e
# ---
# channels:
# - conda-forge
# - bioconda
# dependencies:
# - python
# - quarto
# - jupyter
# - pandas
# - matplotlib
# - papermill
RUN mkdir -p /conda-envs/b933cc1aa7c25db04635e7ec0e37f80e
COPY workflow/envs/quarto.yaml /conda-envs/b933cc1aa7c25db04635e7ec0e37f80e/environment.yaml
# Step 2: Generate conda environments
RUN <<EOR
conda config --add channels nodefaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority strict
EOR
RUN conda env create --no-default-packages --prefix /conda-envs/8b5bbd33d7ccdbbe3a28773771abe2b3 --file /conda-envs/8b5bbd33d7ccdbbe3a28773771abe2b3/environment.yaml
RUN conda env create --no-default-packages --prefix /conda-envs/f24b0ccfc23aadb93b466380cd592733 --file /conda-envs/f24b0ccfc23aadb93b466380cd592733/environment.yaml
RUN conda env create --no-default-packages --prefix /conda-envs/a0a27bbdca540d02023c7fdcf819bfc1 --file /conda-envs/a0a27bbdca540d02023c7fdcf819bfc1/environment.yaml
RUN conda env create --no-default-packages --prefix /conda-envs/a3e2fce7f2f6fdbe1aa97232e3def601 --file /conda-envs/a3e2fce7f2f6fdbe1aa97232e3def601/environment.yaml
RUN conda env create --no-default-packages --prefix /conda-envs/899c0a8c04c6edeed4b242dbc3e0e1c8 --file /conda-envs/899c0a8c04c6edeed4b242dbc3e0e1c8/environment.yaml
RUN conda env create --no-default-packages --prefix /conda-envs/e5aec3a0d6b8921994e5305d4f89e90f --file /conda-envs/e5aec3a0d6b8921994e5305d4f89e90f/environment.yaml
RUN conda env create --no-default-packages --prefix /conda-envs/cb972f023533b03e742da9095ce03b06 --file /conda-envs/cb972f023533b03e742da9095ce03b06/environment.yaml
RUN conda env create --no-default-packages --prefix /conda-envs/a4e1b935cbca52df9b6f192ff86c464c --file /conda-envs/a4e1b935cbca52df9b6f192ff86c464c/environment.yaml
RUN conda env create --no-default-packages --prefix /conda-envs/b933cc1aa7c25db04635e7ec0e37f80e --file /conda-envs/b933cc1aa7c25db04635e7ec0e37f80e/environment.yaml
RUN conda env create --no-default-packages --prefix /conda-envs/ae3e37bf43cbb30416a885168e10c552 --file /conda-envs/ae3e37bf43cbb30416a885168e10c552/environment.yaml
# cleanup when version changed
ARG VERSION
RUN conda clean --all -y