Recipes for building software and submitting jobs on CHTC. Click on the links below to view a list of available options or see the table below for software options:
We welcome contributions and feedback! See below for more details.
| Software Name | Apptainer | Docker | Local Install | HPC Spack |
|---|---|---|---|---|
| Alphafold | X | - | - | - |
| Conda | X | X | - | - |
| Julia | X | - | - | - |
| Matlab | X | X | - | - |
| PALM | X | - | - | - |
| Python | X | X | - | - |
| PyTorch | X | - | - | - |
| R | X | - | - | - |
| SLEAP | X | - | - | - |
| SUMO | X | - | - | - |
You can retrieve the contents of this repository while logged in to CHTC (Connecting to CHTC) following the instructions below.
If you want the whole repository, simply run
git clone https://github.com/CHTC/recipes.git
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.
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
At this time, GitHub does not have a mechanism for retrieving a sub-directory of a repository. Therefore, for cases where a user may want to have an entire directory, we have prepared compressed tarballs for easy retrieval.
Follow the instructions above to retrieve the .tar.gz file within the directory of interest.
Then unpack the compressed directory using the tar command.
For example, the workflows/simple_DAG directory includes the compressed file simple_DAG.tar.gz.
Retrieve the file using the command
wget https://github.com/CHTC/recipes/raw/main/workflows/simple_DAG/simple_DAG.tar.gz
and then unpack the compressed directory with
tar -xzf simple_DAG.tar.gz
If you are interested in contributing to this repository, or have feedback on how we can improve it, please reach out to us at [email protected].