Conda environment definition files for making environments that are useful for various analysis tasks.
Most have been validated to work on NEMO.
The up-to-date version of an environment called <env-name> can be installed with the basic command:
conda env create --force -f https://github.com/scbirlab/envs/raw/main/<env-name>.yml
This can take several minutes to complete. If mamba is installed on your system (as is the case on NEMO),
substituting conda for mamba may be faster.
For example, to install the basic environment:
mamba env create --force -f https://github.com/scbirlab/envs/raw/main/basic.yml
Other versions can be installed by replacing main with the version name, for example v0.0.1:
mamba env create --force -f https://github.com/scbirlab/envs/raw/v0.0.1/basic.yml
This is a general-purpose environment for data analysis, machine learning, and chemistry.
It provides Jupyter Notebooks, rdkit, and GPU versions
of tensorflow, and jax
which are compatible with NEMO.
mamba env create --force -f https://github.com/scbirlab/envs/raw/main/basic.yml
Installs Jupyter Notebooks and GPU version of pytorch and
chemprop compatible with NEMO.
mamba env create --force -f https://github.com/scbirlab/envs/raw/main/chemprop.yml
This is an environment for large language modelling for chemistry.
It provides Jupyter Notebooks, rdkit, and GPU versions
of tensorflow, flax,
pytorch, and 🤗 transformers
which are compatible with NEMO.
mamba env create --force -f https://github.com/scbirlab/envs/raw/main/chem-llm.yml
Installs tools for developing Python packages and other software.
mamba env create --force -f https://github.com/scbirlab/envs/raw/main/dev.yml
Installs hts-tools for analyzing platereader data.
mamba env create --force -f https://github.com/scbirlab/envs/raw/main/hts.yml
Installs monte-barcode and ogilo
for designing barcoded oligo pools.
mamba env create --force -f https://github.com/scbirlab/envs/raw/main/oligo-design.yml
Add to the issue tracker.
Here are the help pages of the software installed in these environments.