docs: conda on dangpu

docs/conda/brickman-chipseq.yml

@@ -0,0 +1,16 @@
+name: brickman-chipseq
+channels:
+  - conda-forge
+  - bioconda
+  - anaconda
+  - defaults
+dependencies:
+  - bioconda::bedtools==2.31.0
+  - bioconda::deeptools==2.31.0
+  - bioconda::homer==4.11
+  - bioconda::intervene==0.6.4
+  - bioconda::macs2==2.2.9.1
+  - bioconda::pygenometracks==3.8
+  - bioconda::seacr==1.3
+  - bioconda::samtools==1.17
+prefix: /projects/dan1/data/Brickman/conda/envs/brickman-chipseq

docs/conda/celloracle-0.12.1.yml

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+name: celloracle-0.12.1
+channels:
+  - conda-forge
+  - bioconda
+  - anaconda
+  - defaults
+dependencies:
+  # mandatory for jupyter
+  - conda-forge::python=3.8
+  - conda-forge::ipykernel
+  - conda-forge::ipywidgets
+  - anaconda::cython
+  - pip
+  - pip:
+    - scipy
+    - numpy
+    - pygsp
+    - celloracle==0.12.1
+prefix: /projects/dan1/data/Brickman/conda/envs/celloracle-0.12.1

docs/dangpu/conda.md

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+# Conda
+
+To install shared `conda` environment for the lab, follow the steps below.
+
+1. Create a configuration file which contains the list of packages you want
+  to use. Use prefix `brickman-<NGS>.yml`
+2. Populate the configuration file
+3. Create the conda environment
+
+```bash
+mamba env create -p /projects/dan1/data/Brickman/conda/envs/brickman-<NGS>.yml -f brickman-<NGS>.yml
+```
+
+## Example case
+
+Configuration for `brickman-chipseq` environment.
+
+``` title="brickman-chipseq.yml"
+--8<-- "./docs/conda/brickman-chipseq.yml"
+```
+
+To install the environment, run
+
+```bash
+mamba env create -p /projects/dan1/data/Brickman/conda/envs/brickman-chipseq -f brickman-chipseq.yml
+```

mkdocs.yml

@@ -26,7 +26,8 @@ markdown_extensions:
       pygments_lang_class: true
   - pymdownx.inlinehilite
   - pymdownx.details
-  - pymdownx.snippets
+  - pymdownx.snippets:
+      base_path: ["."]
   - pymdownx.superfences
   - pymdownx.tasklist:
       custom_checkbox: true