add Dockerfile

Dockerfile

+FROM condaforge/mambaforge:latest
+LABEL io.github.snakemake.containerized="true"
+LABEL io.github.snakemake.conda_env_hash="49e58cca4906e028f46b0ae5f6c1dac3f5dee26aa638b69ea037d04804b01d82"
+
+# Step 1: Retrieve conda environments
+
+# Conda environment:
+#   source: envs/R_scripts.yaml
+#   prefix: /conda-envs/264f76b767c6fb4787a76b073e3c1550
+#   channels:
+#    - bioconda
+#    - conda-forge
+#   dependencies:
+#     - python >=3.10.4
+#     - r-argparse=2.1.5=r41hc72bb7e_0
+#     - r-base >=4.1.3
+#     - r-minpack.lm=1.2_2=r41h1463581_0
+#     - genomescope2=2.0=py310r41hdfd78af_5
+#     - r-dplyr==1.0.9
+#     - r-formattable==0.2.1
+RUN mkdir -p /conda-envs/264f76b767c6fb4787a76b073e3c1550
+COPY envs/R_scripts.yaml /conda-envs/264f76b767c6fb4787a76b073e3c1550/environment.yaml
+
+# Conda environment:
+#   source: envs/busco_and_assembly.yaml
+#   prefix: /conda-envs/4e57ed29df8b6f849000ab15b5c719f2
+#   channels:
+#    - conda-forge
+#    - bioconda
+#    - anaconda
+#    - defaults
+#   dependencies:
+#     - augustus >=3.3
+#     - biopython
+#     - blast >=2.10.1
+#     - fonts-conda-ecosystem
+#     - hmmer >=3.1b2
+#     - metaeuk
+#     - pandas
+#     - prodigal
+#     - python >=3.3
+#     - r-base
+#     - r-ggplot2 >=2.2.1
+#     - sepp >=4.3.10
+#     - wget
+#     - busco == 5.3.0
+RUN mkdir -p /conda-envs/4e57ed29df8b6f849000ab15b5c719f2
+COPY envs/busco_and_assembly.yaml /conda-envs/4e57ed29df8b6f849000ab15b5c719f2/environment.yaml
+
+# Conda environment:
+#   source: envs/merylMerq_2.yaml
+#   prefix: /conda-envs/bac9eedd8f673dc515402b61559f1582
+#   channels:
+#    - bioconda
+#    - defaults
+#    - conda-forge
+#   dependencies:
+#     - merqury == 1.3
+#     - bedtools == 2.29.2
+#     - meryl == 1.3
+#     - cairo == 1.16
+#     - openjdk == 11.0.13
+#     - r-argparse == 2.1.5
+#     - r-base >=4.0,<4.1.0a0
+#     - r-ggplot2=3.3.2=r40hc72bb7e_1
+#     - r-scales == 1.2.0
+#     - samtools == 1.15.1
+#     - xorg-libxrender == 0.9.10
+#     - xorg-libxext == 1.3.4
+#     - xorg-libxau == 1.0.9
+RUN mkdir -p /conda-envs/bac9eedd8f673dc515402b61559f1582
+COPY envs/merylMerq_2.yaml /conda-envs/bac9eedd8f673dc515402b61559f1582/environment.yaml
+
+# Conda environment:
+#   source: envs/pigz.yaml
+#   prefix: /conda-envs/9f8a8ffad4001cd6453433a4ececbe5b
+#   channels:
+#    - anaconda
+#    - bioconda
+#    - conda-forge
+#   dependencies:
+#    - pigz=2.4
+#    - trim-galore=0.6.6
+#    - pandoc=2.11
+#    - multiqc=1.9
+#    - python=3.8.5
+#    - trimmomatic=0.39
+RUN mkdir -p /conda-envs/9f8a8ffad4001cd6453433a4ececbe5b
+COPY envs/pigz.yaml /conda-envs/9f8a8ffad4001cd6453433a4ececbe5b/environment.yaml
+
+# Conda environment:
+#   source: envs/pretext.yaml
+#   prefix: /conda-envs/d0744b07096b67261c96e38bff814c84
+#   channels:
+#    - anaconda
+#    - bioconda
+#    - conda-forge
+#   dependencies:
+#    - pretextmap == 0.1.9
+#    - pretextsnapshot == 0.0.4
+#    - bwa-mem2 == 2.2.1
+#    - samtools == 1.14
+RUN mkdir -p /conda-envs/d0744b07096b67261c96e38bff814c84
+COPY envs/pretext.yaml /conda-envs/d0744b07096b67261c96e38bff814c84/environment.yaml
+
+# Conda environment:
+#   source: envs/python_scripts.yaml
+#   prefix: /conda-envs/4d7a7861b78c18f5b15454f62f5a7f70
+#   channels:
+#    - conda-forge
+#    - bioconda
+#    - anaconda
+#   dependencies:
+#    - python>=3.9.10
+#    - tabulate=0.8.7
+#    - beautifulsoup4=4.9
+#    - mamba=0.15.2
+#    - pandoc=2.15.*
+#    - tectonic
+#    - wkhtmltopdf
+#    - pandas
+#    - numpy
+#    - ghostscript
+RUN mkdir -p /conda-envs/4d7a7861b78c18f5b15454f62f5a7f70
+COPY envs/python_scripts.yaml /conda-envs/4d7a7861b78c18f5b15454f62f5a7f70/environment.yaml
+
+# Step 2: Generate conda environments
+RUN conda config --set remote_read_timeout_secs 600
+RUN conda env create --prefix /conda-envs/264f76b767c6fb4787a76b073e3c1550 --file /conda-envs/264f76b767c6fb4787a76b073e3c1550/environment.yaml && \
+    conda env create --prefix /conda-envs/4e57ed29df8b6f849000ab15b5c719f2 --file /conda-envs/4e57ed29df8b6f849000ab15b5c719f2/environment.yaml && \
+    conda env create --prefix /conda-envs/bac9eedd8f673dc515402b61559f1582 --file /conda-envs/bac9eedd8f673dc515402b61559f1582/environment.yaml && \
+    conda env create --prefix /conda-envs/9f8a8ffad4001cd6453433a4ececbe5b --file /conda-envs/9f8a8ffad4001cd6453433a4ececbe5b/environment.yaml && \
+    conda env create --prefix /conda-envs/d0744b07096b67261c96e38bff814c84 --file /conda-envs/d0744b07096b67261c96e38bff814c84/environment.yaml && \
+    conda env create --prefix /conda-envs/4d7a7861b78c18f5b15454f62f5a7f70 --file /conda-envs/4d7a7861b78c18f5b15454f62f5a7f70/environment.yaml && \
+    conda clean --all -y