bioscanflow

Repository for developing documentation for metabarcoding-based biomonitoring workflows within the framework of Biodiversity Genomics Europe project. Readthedocs page: https://bioscanflow.readthedocs.io/en/latest/index.html#

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'Dockerfile' and 'bioscanflow_env.yml' are for building Docker image for bioinformatics processing of the sequenceing data.

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For developers

This documentation is built throuh Read the Docs, an open-sourced software documentation hosting platform.

Requirements: git, python, sphinx (documentation generator).

1. Check if git is installed (through command line)

git --version

If git is not installed, then install it For Windows: https://git-scm.com/install/windows For Linux: sudo apt install git-all For MacOS: git --version (it will prompt the install)

2. Download github repository

cd C:/Users/user/Desktop  # go to directory where you want to place the github repo
git clone https://github.com/anslan/bioscanflow.git

cd C:/Users/user/Desktop/bioscanflow/docs  # go to downloaded github repo
git checkout develop # Switch to the develop branch!

3. Install sphinx and other requirements: (make sure python is installed)

cd C:/Users/user/Desktop/BGE_biomonitoring_wf/docs  # go to downloaded github repo
python -m pip install -U sphinx
python -m pip install -r requirements.txt


### If you have problems installing as an admin then try:
cd C:/Users/user/Desktop/bioscanflow/docs  # go to github repo
python -m pip install --user sphinx
python -m pip install --user -r requirements.txt

4. Build local page for testing (in bioscanflow/docs)

For Windows:

# in docs dir
.\make.bat html

If you installed sphinx with --user and make.bat doesn't work, use:

# in docs dir
python -m sphinx -M html . _build

For Linux and macOS:

# in docs dir
make html

Open any html file in the "bioscanflow/docs/_build/html" directory to check the page build.

6. Edit the *.rst files as needed. Then build locally (point 4 above) to check the page before pushing.

If changes do not appear, then remove the "_build" folder and build again:

# in docs dir
rm -r _build
.\make.bat html

7. When edis are done, then push changes to github

git add .    # adds all changes 
git commit -m "describe my edits" # add a brief message what was changed
git push     # push changes to github

After the "git push" the webpage will automatically update itself.