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Conda modules

module avail conda-modules/

Conda is an open-source package management and environment management system that is commonly used in the Python programming ecosystem.

Conda allows you to easily install, update, and manage software packages and libraries, including Python packages, data science libraries, and various dependencies. It handles package dependencies and ensures that software is compatible with your environment.

Conda enables you to create isolated environments (aka Conda environments), where you can work on different projects with different sets of packages and dependencies without conflicts. This helps in maintaining a clean and organized development environment.

Conda is platform-agnostic and can be used on various operating systems, including Windows, macOS, and Linux. This makes it easy to share and reproduce environments across different platforms.

Usage

We encourage users to use mambaforge in preference to conda-modules.

As the conda included in the conda-modules module is not recent version and not a very fast one, we recommend users to use mambaforge module instead.
Mamba can access all the environments installed in a conda-modules module, plus some of the newer ones installed solely to mambaforge.
If you consider using conda in order to install a new environment, we recommend to use Mamba installer, too; see also How to install Conda packages.

Under the conda-modules module, there are multiple environments installed.

The basic commands are:

module add conda-modules-py37 # load initial Conda module
conda env list                # list installed environments
conda activate busco          # activate an environment (e.g. busco)
busco --help                  # use selected application
conda deactivate              # quit

Environment-specific notes

fast-bonito_v0.2.2_py3.7

User must specify absolute paths to the python script basecaller.py and to the model file batchsize200_chunksize6000.pb:

python /software/conda-modules/5.3.1/envs/fast-bonito_v0.2.2_py3.7/fast-bonito/basecaller.py \
--model_directory /software/conda-modules/5.3.1/envs/fast-bonito_v0.2.2_py3.7/fast-bonito/models/batchsize200_chunksize6000.pb

ffpenv

$ conda activate ffpenv
$ export LD_LIBRARY_PATH=/software/conda-modules/5.3.1/envs/ffpenv/lib/python3.7/site-packages/PySide2-5.15.2-py3.7-linux-x86_64.egg/PySide2/Qt/lib:/software/conda-modules/5.3.1/lib:/software/conda-modules/5.3.1/envs/ffpenv/lib/
$ ggparam-gui

megalodon

Prepared with Guppy 5.0.15 (CPU and GPU versions) placed in /software/conda-modules/5.3.1/envs/megalodon/bin/ont-guppy-cpu and /software/conda-modules/5.3.1/envs/megalodon/bin/ont-guppy-gpu.

You should accept ONT licence.

GPU version requires CUDA capability 6.0 and higher (PBS parameter gpu_cap=cuda60).

tedensity_v0.9.1_py3.8

Call the main python script process_genome.py with an absolute path: python /software/conda-modules/5.3.1/envs/tedensity_v0.9.1_py3.8/TE_Density/process_genome.py.