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docs: conda on dangpu
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matq007 committed Aug 31, 2023
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16 changes: 16 additions & 0 deletions docs/conda/brickman-chipseq.yml
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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
19 changes: 19 additions & 0 deletions 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
26 changes: 26 additions & 0 deletions 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
```
3 changes: 2 additions & 1 deletion mkdocs.yml
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Expand Up @@ -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
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