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updated local sleap installation instructions
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niksirbi committed Nov 9, 2023
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46 changes: 37 additions & 9 deletions docs/source/data_analysis/HPC-module-SLEAP.md
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```

## Abbreviations
| Acronym | Meaning |
| --- | --- |
| SLEAP | Social LEAP Estimates Animal Poses |
| SWC | Sainsbury Wellcome Centre |
| HPC | High Performance Computing |
| SLURM | Simple Linux Utility for Resource Management |
| GUI | Graphical User Interface |
| Acronym | Meaning |
| ------- | -------------------------------------------- |
| SLEAP | Social LEAP Estimates Animal Poses |
| SWC | Sainsbury Wellcome Centre |
| HPC | High Performance Computing |
| SLURM | Simple Linux Utility for Resource Management |
| GUI | Graphical User Interface |

## Prerequisites

Expand All @@ -30,8 +30,10 @@ Once you are on the HPC gateway node, SLEAP should be listed among the available

```{code-block} console
$ module avail
...
SLEAP/2023-03-13
SLEAP/2023-08-01
...
```
- `SLEAP/2023-03-13` corresponds to `sleap v.1.2.9`
- `SLEAP/2023-08-01` corresponds to `sleap v.1.3.1`
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you will need to use the SLEAP GUI for some steps, such as labelling frames.
Thus, you also need to install SLEAP on your local PC/laptop.

We recommend following the official [SLEAP installation guide](https://sleap.ai/installation.html).
To be on the safe side, ensure that the local installation version matches the one on the cluster.
We recommend following the official [SLEAP installation guide](https://sleap.ai/installation.html). If you already have `conda` installed, you may skip the `mamba` installation steps and opt for installing the `libmamba-solver` for `conda`:

```{code-block} console
$ conda install -n base conda-libmamba-solver
$ conda config --set solver libmamba
```
This will get you the much faster dependency resolution that `mamba` provides, without having to install `mamba` itself.
From `conda` version 23.10 onwards (released in November 2023), `libmamba-solver` [is anyway the default](https://conda.org/blog/2023-11-06-conda-23-10-0-release/).

After that, you can follow the [rest of the SLEAP installation guide](https://sleap.ai/installation.html#conda-package), substituting `conda` for `mamba` in the relevant commands.

::::{tab-set}

:::{tab-item} Windows and Linux
```{code-block} console
$ conda create -y -n sleap -c conda-forge -c nvidia -c sleap -c anaconda sleap=1.3.1
```
:::

:::{tab-item} MacOS X and Apple Silicon
```{code-block} console
$ conda create -y -n sleap -c conda-forge -c anaconda -c sleap sleap=1.3.1
```
:::

::::

You may exchange `sleap=1.3.1` for other versions. To be on the safe side, ensure that your local installation version matches (or is at least close to) the one installed in the cluster module.

### Mount the SWC filesystem on your local PC/laptop
The rest of this guide assumes that you have mounted the SWC filesystem on your local PC/laptop.
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