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update DROP install instructions
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Smith Nicholas committed Nov 8, 2022
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5 changes: 3 additions & 2 deletions README.md
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Expand Up @@ -24,13 +24,14 @@ We recommend using a dedicated conda environment. (installation time: ~ 10min)
mamba create -n drop_env -c conda-forge -c bioconda drop --override-channels
```

In the case of mamba/conda troubles we recommend using the fixed `DROP.yaml` installation file we make available on our [public server](https://www.cmm.in.tum.de/public/paper/drop_analysis/DROP.yaml). Install this using the following command:
In the case of mamba/conda troubles we recommend using the fixed `DROP_<version>.yaml` installation file we make available on our [public server](https://www.cmm.in.tum.de/public/paper/drop_analysis/). Install the current version and use the full path in the following command to install the conda environment `drop_env`
```
mamba env create -f DROP.yaml
mamba env create -f DROP_1.2.2.yaml
```

Test installation with demo project
```
conda activate drop_env
mkdir ~/drop_demo
cd ~/drop_demo
drop demo
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9 changes: 5 additions & 4 deletions docs/source/installation.rst
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Expand Up @@ -15,20 +15,21 @@ For installing, use `mamba` instead of `conda` as it provides more reliable and
mamba create -n drop_env -c conda-forge -c bioconda drop --override-channels
In the case of mamba/conda troubles we recommend using the fixed ``DROP.yaml`` installation file
we make available on our `public server. <https://www.cmm.in.tum.de/public/paper/drop_analysis/DROP.yaml>`_
Install this using the following command:
In the case of mamba/conda troubles we recommend using the fixed ``DROP_<version>.yaml`` installation file
we make available on our `public server. <https://www.cmm.in.tum.de/public/paper/drop_analysis/>`_
Install the current version and use the full path in the following command to install the conda environment ``drop_env``

.. code-block:: bash
mamba env create -f DROP.yaml
mamba env create -f DROP_1.2.2.yaml
Installation time: ~ 10min

Test whether the pipeline runs through by setting up the demo dataset in an empty directory (e.g. ``~/drop_demo``).

.. code-block:: bash
conda activate drop_env
mkdir ~/drop_demo
cd ~/drop_demo
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