udpate to working conda depedancies and save state with a Dockerfile

Dockerfile

@@ -0,0 +1,60 @@
+FROM condaforge/mambaforge:latest
+LABEL io.github.snakemake.containerized="true"
+LABEL io.github.snakemake.conda_env_hash="fd0eeef546ed00fa95ff85a8baf143dfccd52a6183b57e9bb8e972bf196948d5"
+
+# Step 1: Retrieve conda environments
+
+# Conda environment:
+#   source: workflow/envs/R.yaml
+#   prefix: /conda-envs/ee4bfa88159ef77575445596ec2221ce
+#   name: R
+#   channels:
+#     - conda-forge
+#     - r
+#     - defaults
+#   dependencies:
+#     #- xorg-libx11
+#     #- xorg-libxau
+#     #- r::r-ggplot2
+#     - r-base>=4.0
+#     - r-essentials
+#     - r-cairo
+#     - r-data.table
+#     - r-cowplot
+#     - r-argparse>=2.1.2
+#     - r-glue
+#     - r-r.utils
+#     - r-rcolorbrewer
+#     - r-scales
+#     - r-tidyverse>=1.3.0
+RUN mkdir -p /conda-envs/ee4bfa88159ef77575445596ec2221ce
+COPY workflow/envs/R.yaml /conda-envs/ee4bfa88159ef77575445596ec2221ce/environment.yaml
+
+# Conda environment:
+#   source: workflow/envs/env.yaml
+#   prefix: /conda-envs/5ea0207c595d8a051ab13a13766b14f6
+#   name: python_and_cli_env
+#   channels:
+#     - conda-forge
+#     - bioconda
+#     - defaults
+#   dependencies:
+#     - numpy<1.20
+#     - numba
+#     - cooler<=0.8.11
+#     - pandas<=1.5
+#     - minimap2==2.18
+#     - bioconda::bedtools
+#     - bioconda::samtools>=1.14
+#     - bioconda::htslib>=1.14
+#     - bioconda::pysam>=0.15.0
+#     - bioconda::bwa
+#     - pigz
+RUN mkdir -p /conda-envs/5ea0207c595d8a051ab13a13766b14f6
+COPY workflow/envs/env.yaml /conda-envs/5ea0207c595d8a051ab13a13766b14f6/environment.yaml
+
+# Step 2: Generate conda environments
+
+RUN mamba env create --prefix /conda-envs/ee4bfa88159ef77575445596ec2221ce --file /conda-envs/ee4bfa88159ef77575445596ec2221ce/environment.yaml && \
+    mamba env create --prefix /conda-envs/5ea0207c595d8a051ab13a13766b14f6 --file /conda-envs/5ea0207c595d8a051ab13a13766b14f6/environment.yaml && \
+    mamba clean --all -y

workflow/envs/env.yaml

@@ -1,18 +1,17 @@
 name: python_and_cli_env
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
   - defaults
 dependencies:
-  - numpy<=1.29
+  - numpy<1.20
   - numba
-  - cooler==0.8.11
+  - cooler<=0.8.11
   - pandas<=1.5
   - minimap2==2.18
-  - bedtools
-  - samtools>=1.14
-  - pysam>=0.15.0
-  - snakemake>=7.25.0
-  - snakefmt
-  - bwa
+  - bioconda::bedtools
+  - bioconda::samtools>=1.14
+  - bioconda::htslib>=1.14
+  - bioconda::pysam>=0.15.0
+  - bioconda::bwa
   - pigz