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The CBBL tools repository

The CBBL tools github repo is a collection of tools that the CBBL members have developed to help dealing with usual tasks. The repository is not perfect, nor nicely updated... It represents a starting point to face some typical tasks when dealing with bioinformatics, computational chemistry, molecular simulations, etc...

This is a live repository, always to be improved. Either if you are a member of the CBBL or not, you contribution is more than welcome.

How to use the repository

Most folders contain either notebooks, small scripts, or both. The intended workflow is:

  1. Enter the folder that matches your topic.
  2. Read its local Readme.md or README.md.
  3. Run the notebooks for interactive examples or the scripts for lightweight command-line tasks.

The sequenceTools folder combines notebook-based workflows with command-line scripts for focused sequence analyses. The rest of the folders keep their existing scripts and notebooks, and each active tools folder also includes:

  • report_<folder>.tex: a LaTeX summary of the methods used in that folder.

The reports now use pure LaTeX/TikZ for conceptual schemes. Notebooks in the repo should only exist when they perform the actual computational or teaching work of the folder.

Installing requirements

Most folders include a local environment.yml with the Python packages needed for that workflow. Use the environment closest to the material you want to run. For example:

conda env create -f sequenceTools/environment.yml
conda activate tools-sequencetools

Some subfolders also provide a more specific environment.yml for command-line tools or focused workflows:

conda env create -f sequenceTools/proteinSequenceTools/environment.yml
conda activate tools-protein-sequence-tools

For non-conda workflows, some folders may also include a requirements.txt file:

python3 -m pip install -r path/to/requirements.txt

Folder-specific setup notes, external software requirements and known limitations are documented in each folder README. Graphical applications or research codes such as ChimeraX or ProteinMPNN may require separate installation steps.

How to generate the reports

The repository uses a common root .latexmkrc so that every report is compiled with latexmk using lualatex.

Prerequisites:

  • jupyter
  • latexmk
  • a TeX distribution with lualatex
  • Python packages from requirements.txt

To build every report from the root of the repo:

python build_reports.py

This runs latexmk in each top-level tools folder with the shared root .latexmkrc, using lualatex.

To build a single report manually, go to the target folder and run:

latexmk -r ../.latexmkrc -lualatex report_<folder>.tex

For example, in sequenceTools the report file is report_sequenceTools.tex.

Instructions to build the HTML site

The repo contains an HTML site that can be accessed through this link. To build the site when updating the material of the repo, you should install jupyter book and ghp-import, to make the handling of the gh-pages branch easier. In short, once installed and assuming that your local repo copy is <local_github>/Tools do the following:

cd <local_github>
jb build Tools; cd Tools; git add .; git commit -m "update"; git push; ghp-import -n -p -f _build/html