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Conda/Mamba modules

module avail mambaforge/       # preferred option
module avail conda-modules/    # obsolete

Conda/Mamba are open-source package management and environment management systems that is commonly used in the Python programming ecosystem.

Conda/Mamba 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. Their syntax is basically the same.

Conda/Mamba enables you to create isolated 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.

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

As the conda included in the conda-modules module is obsolete and slow, we recommend to use mambaforge module instead to new environments. The mambaforge module contains mqamba package manager as well as newer version of conda package installer.
Mamba can access all the environments installed in a conda-modules module, plus some of the newer ones installed solely to mambaforge.

Warning

Avoid combining Conda/Mamba environments with traditional modules in a single session. Doing so can often lead to conflicts and application malfunctions.

Usage

Use existing environment

The basic commands are:

module add mambaforge     # load the module
mamba env list            # list installed environments
mamba activate busco      # activate an environment (e.g. busco)
mamba --help              # use selected application
mamba deactivate          # quit

Install new environment

See How to install Conda/Mamba packages.

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.