Installation¶
We recommend running bulkvis from within a python virtual environment so that there are no conflicts in dependencies.
Installing pip¶
pip is most likely already installed, to find out run:
pip --version
If pip is not installed, use the official get-pip.py script.
Create and activate a virtual environment¶
For linux and MacOS:
python3 -m venv bulkvis-env
source bulkvis-env/bin/activate
For Windows:
python3 -m venv bulkvis
bulkvis\Scripts\activate
If the virtual environment is successfully activated the prefix (bulkvis) will be present.
Running deactivate will deactivate and exit the virtual environment
Clone bulkvis¶
bulkvis can be retrieved by cloning the git repository:
git clone https://github.com/LooseLab/bulkvis.git
or by navigating to bulkvis and downloading an zip of the repository, this will then need to be unzipped.
Installing dependencies¶
Once the repository is cloned or downloaded bulkvis’ dependencies will need to be installed. This must be run from within the virtual environment to prevent conflicts. Run:
pip install -r bulkvis/requirements.txt
This will fetch and install all the required packages.
Creating config.ini¶
bulkvis uses a configuration file, config.ini, to provide global variables that are required for operation. A config
file can either be generated by running utils/set_config.py (requires a bulkfile) or by copying and editing an
example bulkfile from config.md.
Using set_config.py:
cd bulkvis
python utils/set_confi.py -b <<bulkfile>> -i /path/to/bulkfile/directory -e /path/to/readfile/directory -m /path/to/mapfile/directory -c config.ini
Using config.md:
cd bulkvis
touch config.ini
nano config.ini
Then navigate to config.md, copy and paste the example
configuration settings into nano in the terminal and finally change the directories (dir, out and map) to point
towards your bulk-fast5-files and a read directory.