howto:bioinformatics
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howto:bioinformatics [2025/05/06 11:21] nmfuphi [Need Help?] |
howto:bioinformatics [2025/05/21 10:50] (current) nmfuphi [Singularity] |
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| === Shared Conda Environments === | === Shared Conda Environments === | ||
| - | For most use cases — especially in bioinformatics | + | For most use cases, especially in bioinformatics, CHPC provides pre-built, **shared Conda environments** installed under: |
| '/ | '/ | ||
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| module load conda_init | module load conda_init | ||
| </ | </ | ||
| + | |||
| + | The second module updates your .bashrc file by adding necessary shell variables. | ||
| + | To apply these changes, you can either log out and log back in, or run: <code bash> | ||
| + | After this setup, you won’t need to load additional modules for your jobs—only the eval and conda activate steps are required. | ||
| === Step 2: Initialize Conda in your shell === | === Step 2: Initialize Conda in your shell === | ||
| Line 246: | Line 250: | ||
| If you need software that is not included in the shared environments, | If you need software that is not included in the shared environments, | ||
| - | > **Important: | + | > **Important: |
| === Step-by-step setup === | === Step-by-step setup === | ||
| + | ssh to username@scp.chpc.ac.za, | ||
| === Step 1: Load Conda === | === Step 1: Load Conda === | ||
| <code bash> | <code bash> | ||
| Line 303: | Line 307: | ||
| * ✅ Use **shared environments** whenever possible for consistency and faster setup. | * ✅ Use **shared environments** whenever possible for consistency and faster setup. | ||
| * 📁 Create private environments **only in Lustre** directories, | * 📁 Create private environments **only in Lustre** directories, | ||
| - | * ⚠️ Do **not** use Conda in your '' | + | * ⚠️ Do **not** use Conda in your '' |
| * 📌 Use the '' | * 📌 Use the '' | ||
| * 🧼 Periodically clean up unused environments with `conda remove --all`. | * 🧼 Periodically clean up unused environments with `conda remove --all`. | ||
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| #PBS -N singularity_job | #PBS -N singularity_job | ||
| #PBS -q normal | #PBS -q normal | ||
| - | #PBS -l select=1: | + | #PBS -l select=1: |
| #PBS -l walltime=12: | #PBS -l walltime=12: | ||
| #PBS -o singularity_output.log | #PBS -o singularity_output.log | ||
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| </ | </ | ||
| - | ===== Nextflow | + | ==== Nextflow ==== |
| Nextflow is a free and open-source workflow management system that enables the development and execution of data analysis pipelines. It simplifies complex computational workflows and ensures reproducibility, | Nextflow is a free and open-source workflow management system that enables the development and execution of data analysis pipelines. It simplifies complex computational workflows and ensures reproducibility, | ||
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