Small installation issues

[thendriks]

When following along with the installation instructions (https://d2s.semanticscience.org/docs/d2s-installation) I ran into a couple of issues using MacOS:

• pipx install benten --python python3.7 yields no such file error. Should probably be pipx --python python3.7 install benten
• pipx install d2s cwlref-runner yields unrecognized arguments, though installing the packages one after the other works. Strange as this should work accoring to the documentation.
• Pipx install instructions are provided before pipx commands. May be a stylistic choice to give more importance to d2s?

[vemonet]

• Benten was (still is?) really experimental, I installed and wrote the documentation literally the day it was announced in the CWL community, because I happened to attend the CWL community call where its creator presented it. We might need to update the install and add a tag to warn the tool is in development and installation instructions might need to be updated ("see reference install URL")

• for the pipx install d2s cwlref-runner I was not sure about which path to take and was waiting for feedback from user to see how to improve it. I agree that the current is quite confusing and not really streamlined

I think the best is that people should use what they usually use to install python packages globally (so pip or pip3 usually). But pip version handling and isolation is still quite bad, so I figured out if you just want to install a single isolated version of a pip package the best is to use pipx (still not perfect, but quite good and supported by the main Python community)

We might want to rewrite it like this:

• If you already use pip to install your python package just use it: pip install ...
• If you don't know what I am talking about and think I probably made a typo to "pipe":
  • Instructions to install pipx
  • Instal d2s and cwlref-runner using pipx (or just pip if we want to keep things simple and avoid introducing additional tool not common)