Initial commit

.docker/README.md

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+# Dockerfiles for each version (>= v0.7.0)
+
+This directory contains Dockerfiles associated with each release. 
+
+The Docker image derived from this file contains all Conda environments for each rule, i.e. the whole workflow is run in one image.
+
+These images are shared via [Docker Hub](https://hub.docker.com/repository/docker/niekwit/rna-seq-salmon-deseq2/general) and are generated as follows (from directory with workflow code):
+
+```shell
+$ snakemake --containerize > Dockerfile
+$ sudo docker build -t niekwit/rna-seq-salmon-deseq2:{VERSION} .
+$ sudo docker login
+$ sudo docker push niekwit/rna-seq-salmon-deseq2:{VERSION}
+```

.docker/v0.7.0/Dockerfile

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+FROM condaforge/mambaforge:latest
+LABEL io.github.snakemake.containerized="true"
+LABEL io.github.snakemake.conda_env_hash="c640e836d0014ff13323253b1efe636acdc33f7708db803896fb083e161c5f5f"
+
+# Step 1: Retrieve conda environments
+
+# Conda environment:
+#   source: https://github.com/snakemake/snakemake-wrappers/raw/v3.12.0/bio/fastqc/environment.yaml
+#   prefix: /conda-envs/90ea9a0a5f4de478eb6aa43932774175
+#   channels:
+#     - conda-forge
+#     - bioconda
+#     - nodefaults
+#   dependencies:
+#     - fastqc =0.12.1
+#     - snakemake-wrapper-utils =0.6.2
+RUN mkdir -p /conda-envs/90ea9a0a5f4de478eb6aa43932774175
+ADD https://github.com/snakemake/snakemake-wrappers/raw/v3.12.0/bio/fastqc/environment.yaml /conda-envs/90ea9a0a5f4de478eb6aa43932774175/environment.yaml
+
+# Conda environment:
+#   source: https://github.com/snakemake/snakemake-wrappers/raw/v3.12.0/bio/salmon/decoys/environment.yaml
+#   prefix: /conda-envs/8456381e797f1c0d40a30d5587f38aeb
+#   channels:
+#     - conda-forge
+#     - nodefaults
+#   dependencies:
+#     - bzip2 =1.0.8
+#     - gzip =1.13
+RUN mkdir -p /conda-envs/8456381e797f1c0d40a30d5587f38aeb
+ADD https://github.com/snakemake/snakemake-wrappers/raw/v3.12.0/bio/salmon/decoys/environment.yaml /conda-envs/8456381e797f1c0d40a30d5587f38aeb/environment.yaml
+
+# Conda environment:
+#   source: https://github.com/snakemake/snakemake-wrappers/raw/v3.12.0/bio/salmon/index/environment.yaml
+#   prefix: /conda-envs/e4a3325e8ed88fd69ecfc27669ef70eb
+#   channels:
+#     - conda-forge
+#     - bioconda
+#     - nodefaults
+#   dependencies:
+#     - salmon =1.10.3
+RUN mkdir -p /conda-envs/e4a3325e8ed88fd69ecfc27669ef70eb
+ADD https://github.com/snakemake/snakemake-wrappers/raw/v3.12.0/bio/salmon/index/environment.yaml /conda-envs/e4a3325e8ed88fd69ecfc27669ef70eb/environment.yaml
+
+# Conda environment:
+#   source: https://github.com/snakemake/snakemake-wrappers/raw/v3.12.0/bio/salmon/quant/environment.yaml
+#   prefix: /conda-envs/1193c2e35bb44028f63ef3ca20567daa
+#   channels:
+#     - bioconda
+#     - conda-forge
+#     - nodefaults
+#   dependencies:
+#     - salmon =1.10.3
+#     - gzip =1.13
+#     - bzip2 =1.0.8
+RUN mkdir -p /conda-envs/1193c2e35bb44028f63ef3ca20567daa
+ADD https://github.com/snakemake/snakemake-wrappers/raw/v3.12.0/bio/salmon/quant/environment.yaml /conda-envs/1193c2e35bb44028f63ef3ca20567daa/environment.yaml
+
+# Conda environment:
+#   source: https://github.com/snakemake/snakemake-wrappers/raw/v3.12.0/bio/trim_galore/pe/environment.yaml
+#   prefix: /conda-envs/7c8f9db6001702ef40e5b666df2ea0f5
+#   channels:
+#     - conda-forge
+#     - bioconda
+#     - nodefaults
+#   dependencies:
+#     - trim-galore =0.6.10
+RUN mkdir -p /conda-envs/7c8f9db6001702ef40e5b666df2ea0f5
+ADD https://github.com/snakemake/snakemake-wrappers/raw/v3.12.0/bio/trim_galore/pe/environment.yaml /conda-envs/7c8f9db6001702ef40e5b666df2ea0f5/environment.yaml
+
+# Conda environment:
+#   source: workflow/envs/deseq2.yml
+#   prefix: /conda-envs/d979651088006f3fb08a629a8ebd8bdf
+#   name: deseq2
+#   channels: 
+#     - conda-forge
+#     - bioconda
+#     - defaults
+#   dependencies:
+#     - r-base=4.2
+#     - r-rcolorbrewer=1.1_3
+#     - r-dplyr=1.1.2
+#     - r-pheatmap=1.0.12
+#     - r-stringr=1.5.0
+#     - r-ggplot2=3.4.2
+#     - r-cowplot=1.1.1
+#     - r-readr=2.1.4
+#     - r-readxl=1.4.2
+#     - r-openxlsx=4.2.5
+#     - r-foreach=1.5.2
+#     - r-ggrepel=0.9.3
+#     - bioconductor-deseq2=1.38.0
+#     - bioconductor-genomicfeatures=1.50.2
+#     - bioconductor-tximport=1.26.0
+#     - r-ggfortify=0.4.16
+#     - bioconductor-limma=3.54.0
+#     - bioconductor-rtracklayer=1.58.0
+RUN mkdir -p /conda-envs/d979651088006f3fb08a629a8ebd8bdf
+COPY workflow/envs/deseq2.yml /conda-envs/d979651088006f3fb08a629a8ebd8bdf/environment.yaml
+
+# Conda environment:
+#   source: workflow/envs/resources.yml
+#   prefix: /conda-envs/e5d9fbb7bf25e32fd9c4c7d06bdf9507
+#   name: deseq2
+#   channels: 
+#     - conda-forge
+#     - bioconda
+#     - defaults
+#   dependencies:
+#     - python=3.11
+#     - multiqc=1.20
+#     - pigz=2.8
+#     - salmon=1.10.2
+RUN mkdir -p /conda-envs/e5d9fbb7bf25e32fd9c4c7d06bdf9507
+COPY workflow/envs/resources.yml /conda-envs/e5d9fbb7bf25e32fd9c4c7d06bdf9507/environment.yaml
+
+# Step 2: Generate conda environments
+
+RUN mamba env create --prefix /conda-envs/90ea9a0a5f4de478eb6aa43932774175 --file /conda-envs/90ea9a0a5f4de478eb6aa43932774175/environment.yaml && \
+    mamba env create --prefix /conda-envs/8456381e797f1c0d40a30d5587f38aeb --file /conda-envs/8456381e797f1c0d40a30d5587f38aeb/environment.yaml && \
+    mamba env create --prefix /conda-envs/e4a3325e8ed88fd69ecfc27669ef70eb --file /conda-envs/e4a3325e8ed88fd69ecfc27669ef70eb/environment.yaml && \
+    mamba env create --prefix /conda-envs/1193c2e35bb44028f63ef3ca20567daa --file /conda-envs/1193c2e35bb44028f63ef3ca20567daa/environment.yaml && \
+    mamba env create --prefix /conda-envs/7c8f9db6001702ef40e5b666df2ea0f5 --file /conda-envs/7c8f9db6001702ef40e5b666df2ea0f5/environment.yaml && \
+    mamba env create --prefix /conda-envs/d979651088006f3fb08a629a8ebd8bdf --file /conda-envs/d979651088006f3fb08a629a8ebd8bdf/environment.yaml && \
+    mamba env create --prefix /conda-envs/e5d9fbb7bf25e32fd9c4c7d06bdf9507 --file /conda-envs/e5d9fbb7bf25e32fd9c4c7d06bdf9507/environment.yaml && \
+    mamba clean --all -y