feat: update Dockerfile

Dockerfile

@@ -0,0 +1,185 @@
+FROM condaforge/mambaforge:latest
+LABEL io.github.snakemake.containerized="true"
+LABEL io.github.snakemake.conda_env_hash="513bdb2b4084511fb27cc35dd917700337f86ce6b26566dfe6049b47ebc4a3f7"
+
+# Step 1: Retrieve conda environments
+
+# Conda environment:
+#   source: ../workflow/env/R.yml
+#   prefix: /conda-envs/40cdd57d2470dfd817a34e1ec7edeaa4
+#   channels:
+#     - conda-forge
+#     - r
+#     - bioconda
+#   dependencies:
+#     - r-base=4.0.3
+#     - r-hexbin
+#     - r-data.table
+#     - r-pheatmap
+#     - r-hmisc
+#     - r-latticeextra
+#     - r-r.utils
+#     - r-scales
+#     - r-rcurl
+#     - r-ggplot2
+#     - r-openxlsx
+#     - r-knitr
+#     - r-rmarkdown
+#     - r-tidyverse
+#     - bioconductor-deseq2
+#     - bioconductor-rtracklayer
+#     - bioconductor-topgo
+#     - bioconductor-vsn
+#     - bioconductor-apeglm
+#     - bioconductor-reactomepa
+RUN mkdir -p /conda-envs/40cdd57d2470dfd817a34e1ec7edeaa4
+COPY ../workflow/env/R.yml /conda-envs/40cdd57d2470dfd817a34e1ec7edeaa4/environment.yaml
+
+# Conda environment:
+#   source: ../workflow/env/alignment.yml
+#   prefix: /conda-envs/8e96037ab9b9dd95318e6dde69e1b470
+#   channels:
+#     - bioconda
+#   dependencies:
+#     - star=2.7.6a
+#     - subread=2.0.1
+RUN mkdir -p /conda-envs/8e96037ab9b9dd95318e6dde69e1b470
+COPY ../workflow/env/alignment.yml /conda-envs/8e96037ab9b9dd95318e6dde69e1b470/environment.yaml
+
+# Conda environment:
+#   source: ../workflow/env/bash.yml
+#   prefix: /conda-envs/16e1dc5e3e5976d71e955eaf12ac9181
+#   channels:
+#     - conda-forge
+#   dependencies:
+#     - bash=5.1.16
+RUN mkdir -p /conda-envs/16e1dc5e3e5976d71e955eaf12ac9181
+COPY ../workflow/env/bash.yml /conda-envs/16e1dc5e3e5976d71e955eaf12ac9181/environment.yaml
+
+# Conda environment:
+#   source: ../workflow/env/bedtools.yml
+#   prefix: /conda-envs/7548059a7c044c6fa179ed2c582570cb
+#   channels:
+#     - bioconda
+#   dependencies:
+#     - bedtools=2.30.0
+RUN mkdir -p /conda-envs/7548059a7c044c6fa179ed2c582570cb
+COPY ../workflow/env/bedtools.yml /conda-envs/7548059a7c044c6fa179ed2c582570cb/environment.yaml
+
+# Conda environment:
+#   source: ../workflow/env/deeptools.yml
+#   prefix: /conda-envs/2f716f46231f821a5e905c39c6060cff
+#   channels:
+#     - conda-forge
+#     - bioconda
+#   dependencies:
+#     - deeptools=3.5.1
+RUN mkdir -p /conda-envs/2f716f46231f821a5e905c39c6060cff
+COPY ../workflow/env/deeptools.yml /conda-envs/2f716f46231f821a5e905c39c6060cff/environment.yaml
+
+# Conda environment:
+#   source: ../workflow/env/pandas.yml
+#   prefix: /conda-envs/50d812d8ce9078db884e008cdd1ec8ab
+#   channels:
+#     - conda-forge
+#     - anaconda
+#   dependencies:
+#     - pandas=2.2.1
+RUN mkdir -p /conda-envs/50d812d8ce9078db884e008cdd1ec8ab
+COPY ../workflow/env/pandas.yml /conda-envs/50d812d8ce9078db884e008cdd1ec8ab/environment.yaml
+
+# Conda environment:
+#   source: ../workflow/env/picard.yml
+#   prefix: /conda-envs/5802f2d84ae022c00e054e6c16564f06
+#   channels:
+#     - bioconda
+#   dependencies:
+#     - picard=2.27.4
+RUN mkdir -p /conda-envs/5802f2d84ae022c00e054e6c16564f06
+COPY ../workflow/env/picard.yml /conda-envs/5802f2d84ae022c00e054e6c16564f06/environment.yaml
+
+# Conda environment:
+#   source: ../workflow/env/qc.yml
+#   prefix: /conda-envs/c9db25f4fb5a47a64d4be70e476fd582
+#   channels:
+#     - conda-forge
+#     - bioconda
+#   dependencies:
+#     - python=3.11 # fix multiqc imp import error
+#     - fastqc=0.11.9
+#     - multiqc=1.14
+RUN mkdir -p /conda-envs/c9db25f4fb5a47a64d4be70e476fd582
+COPY ../workflow/env/qc.yml /conda-envs/c9db25f4fb5a47a64d4be70e476fd582/environment.yaml
+
+# Conda environment:
+#   source: ../workflow/env/samtools.yml
+#   prefix: /conda-envs/9a7384898f8f9aa25cd1d29f531a7f7d
+#   channels:
+#     - conda-forge
+#     - bioconda
+#   dependencies:
+#     - samtools=1.16.1
+#     - ucsc-gtftogenepred=447
+#     - ucsc-genepredtobed=447
+RUN mkdir -p /conda-envs/9a7384898f8f9aa25cd1d29f531a7f7d
+COPY ../workflow/env/samtools.yml /conda-envs/9a7384898f8f9aa25cd1d29f531a7f7d/environment.yaml
+
+# Conda environment:
+#   source: ../workflow/env/trimmomatic.yml
+#   prefix: /conda-envs/b93daf96b2454232db6380819bb61725
+#   channels:
+#     - bioconda
+#   dependencies:
+#     - trimmomatic=0.39
+RUN mkdir -p /conda-envs/b93daf96b2454232db6380819bb61725
+COPY ../workflow/env/trimmomatic.yml /conda-envs/b93daf96b2454232db6380819bb61725/environment.yaml
+
+# Conda environment:
+#   source: ../workflow/env/wget.yml
+#   prefix: /conda-envs/8deaf44f9ffd29816443812db4b8bb83
+#   channels:
+#     - anaconda
+#     - conda-forge
+#   dependencies:
+#     - wget=1.21.3
+#     - gzip
+RUN mkdir -p /conda-envs/8deaf44f9ffd29816443812db4b8bb83
+COPY ../workflow/env/wget.yml /conda-envs/8deaf44f9ffd29816443812db4b8bb83/environment.yaml
+
+# Conda environment:
+#   source: ../workflow/env/yte.yml
+#   prefix: /conda-envs/3674dd77e0957c12c05158a88113106a
+#   channels:
+#     - conda-forge
+#   dependencies:
+#     - yte=1.5.1
+RUN mkdir -p /conda-envs/3674dd77e0957c12c05158a88113106a
+COPY ../workflow/env/yte.yml /conda-envs/3674dd77e0957c12c05158a88113106a/environment.yaml
+
+# Conda environment:
+#   source: https://github.com/snakemake/snakemake-wrappers/raw/v2.6.0/utils/datavzrd/environment.yaml
+#   prefix: /conda-envs/346c7adef34200145d01dda184ac25b8
+#   channels:
+#     - conda-forge
+#     - nodefaults
+#   dependencies:
+#     - datavzrd =2.23.8
+RUN mkdir -p /conda-envs/346c7adef34200145d01dda184ac25b8
+ADD https://github.com/snakemake/snakemake-wrappers/raw/v2.6.0/utils/datavzrd/environment.yaml /conda-envs/346c7adef34200145d01dda184ac25b8/environment.yaml
+
+# Step 2: Generate conda environments
+
+RUN mamba env create --prefix /conda-envs/40cdd57d2470dfd817a34e1ec7edeaa4 --file /conda-envs/40cdd57d2470dfd817a34e1ec7edeaa4/environment.yaml && \
+    mamba env create --prefix /conda-envs/8e96037ab9b9dd95318e6dde69e1b470 --file /conda-envs/8e96037ab9b9dd95318e6dde69e1b470/environment.yaml && \
+    mamba env create --prefix /conda-envs/16e1dc5e3e5976d71e955eaf12ac9181 --file /conda-envs/16e1dc5e3e5976d71e955eaf12ac9181/environment.yaml && \
+    mamba env create --prefix /conda-envs/7548059a7c044c6fa179ed2c582570cb --file /conda-envs/7548059a7c044c6fa179ed2c582570cb/environment.yaml && \
+    mamba env create --prefix /conda-envs/2f716f46231f821a5e905c39c6060cff --file /conda-envs/2f716f46231f821a5e905c39c6060cff/environment.yaml && \
+    mamba env create --prefix /conda-envs/50d812d8ce9078db884e008cdd1ec8ab --file /conda-envs/50d812d8ce9078db884e008cdd1ec8ab/environment.yaml && \
+    mamba env create --prefix /conda-envs/5802f2d84ae022c00e054e6c16564f06 --file /conda-envs/5802f2d84ae022c00e054e6c16564f06/environment.yaml && \
+    mamba env create --prefix /conda-envs/c9db25f4fb5a47a64d4be70e476fd582 --file /conda-envs/c9db25f4fb5a47a64d4be70e476fd582/environment.yaml && \
+    mamba env create --prefix /conda-envs/9a7384898f8f9aa25cd1d29f531a7f7d --file /conda-envs/9a7384898f8f9aa25cd1d29f531a7f7d/environment.yaml && \
+    mamba env create --prefix /conda-envs/b93daf96b2454232db6380819bb61725 --file /conda-envs/b93daf96b2454232db6380819bb61725/environment.yaml && \
+    mamba env create --prefix /conda-envs/8deaf44f9ffd29816443812db4b8bb83 --file /conda-envs/8deaf44f9ffd29816443812db4b8bb83/environment.yaml && \
+    mamba env create --prefix /conda-envs/3674dd77e0957c12c05158a88113106a --file /conda-envs/3674dd77e0957c12c05158a88113106a/environment.yaml && \
+    mamba env create --prefix /conda-envs/346c7adef34200145d01dda184ac25b8 --file /conda-envs/346c7adef34200145d01dda184ac25b8/environment.yaml && \
+    mamba clean --all -y