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Recipes for building software and submitting jobs on CHTC

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# CHTC Recipes for Software Installation and Job Submission

Recipes for building software and submitting jobs on [CHTC](https://chtc.cs.wisc.edu). 
Click on the links below to view a list of available options or see the table below 
for software options:

* [Software](software)
* [HPC Workflows](workflows-hpc)
* [HTC Workflows](workflows-htc)

We welcome contributions and feedback! [See below](#contributions-and-feedback) for more details.

## Software List

| Software Name | Apptainer | Docker | Local Install | HPC Spack | 
| :--- | :---: | :---: | :---: | :---: |
| [Alphafold](/software/AlphaFold) | X | - | - | - | 
| [Conda](/software/Conda) | X | X | - | - | 
| [Julia](/software/Julia) | X | X | - | - | 
| [Matlab](/software/Matlab) | X | X | - | - | 
| [PALM](/software/PALM) | X | - | - | - | 
| [Python](/software/Python) | X | X | - | - | 
| [PyTorch](/software/PyTorch) | X | X | - | - | 
| [R](/software/R) | X | X | - | - | 
| [SLEAP](/software/SLEAP) | X | - | - | - |
| [SUMO](/software/SUMO) | X | X | - | - |

## Retrieving Repository Contents from CHTC

You can retrieve the contents of this repository while logged in to CHTC ([Connecting to CHTC](https://chtc.cs.wisc.edu/uw-research-computing/connecting)) following the instructions below.

1. [Whole repository](#whole-repository)
2. [Individual files](#individual-files)

### 1. Whole repository

If you want the whole repository, simply run

```
git clone https://github.com/CHTC/recipes.git
```

### 2. Individual files

Individual files can be retrieved using the URL `https://github.com/CHTC/recipes/raw/main/` in combination with the relative path to the file within the repository.

First, identify the repository path to the file or directory that you are interested in using.
Next, combine the first half of the URL with the relative path to the desired file to yield the full URL.
Finally, use the `wget` command with the full URL to download the file directly to the server you are logged in to.

For example, the simple example definition file `simple_apptainer.def` is located in [/software/guide\_examples](/software/guide_examples).
Thus, the repository path is `/software/guide_examples/simple_apptainer.def`.
The full URL is then given by `https://github.com/CHTC/recipes/raw/main/software/guide_examples/simple_apptainer.def`.
The command to retrieve the file is

```
wget https://github.com/CHTC/recipes/raw/main/software/guide_examples/simple_apptainer.def
```

Alternatively, you can navigate to the file you want in the web browser, and right-click on "Raw" and Copy Link Address. Then, while logged in CHTC, type `wget`, paste in the link, then hit enter to download the file directly.

![Alt text](https://raw.githubusercontent.com/CHTC/recipes/main/docs/getfileURL.png "How to retrieve a URL for direct download")

## Contributions and Feedback

If you are interested in contributing to this repository, or have feedback on how we can improve it, please reach out 
to us at chtc@cs.wisc.edu.

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