Installation for linux - Note

[KrishnaTO]

Noting some instructions I used for installing on a linux server, if want to add to readme.

Works with Biomappings version = 0.1.3-dev

On Ubuntu 18.04+ [on fresh server]:

py_36 () {
  cur_path=ls
  cd /usr/bin
  sudo unlink python
  sudo ln -s /usr/bin/python3.6 python
  python --version
  cd cur_path
}

On Ubuntu 20.04+:

sudo apt update
sudo apt install python-is-python3

Install biomappings:

git clone git+https://github.com/biopragmatics/biomappings.git
# py_36
cd biomappings
sudo apt update
sudo apt install python3-pip
sudo pip install --upgrade setuptools pystow bioregistry pyobo gilda indra rdflib
sudo pip install -e .[web]
biomappings web

[bgyori]

Hi @KrishnaTO, thanks for the note! It looks like these are general instructions for setting up Python and pip on Linux that would be necessary for working with Python packages more generally. So I think it might fall outside the scope of what we document here.

[KrishnaTO]

@bgyori No prob on adding to documentation then (everyone caters to different audience levels); Can still be used for getting it up and running on a cloud server quickly.

Will close issue now

[KrishnaTO]

sudo pip install --upgrade setuptools pystow bioregistry pyobo gilda indra rdflib

is what I should have originally added, which is the critical part.

[bgyori]

The required dependencies (e.g., pystow, etc.) for biomappings are given here as part of the setup configuration: https://github.com/biopragmatics/biomappings/blob/master/setup.cfg#L47-L54 which means that pip install biomappings will install these for you along with the biomappings package itself.

[KrishnaTO]

Note that although the pip install biomappings or instructions in the readme pip install -e .[web] are sufficient to 'run' the webpage, these nor mentioned setup configurations are sufficient for running the scripts to make the predictions.

I think there is great value here.