missing requirements.txt

[olisteadman]

Would you consider including a list of dependencies/packages so the user can get up-and-running more quickly... or at least README.md in this repo to explain whether this necessary?

[emzodls]

The dependencies should be in the manual. I do need to update this though.

[olisteadman]

Nothing in the manual I'm afraid:

[olisteadman]

In order to inform writing of requirements.txt, the list of packages I needed includes the following (this is as far as I've got; am now facing an error in attempted installation of bx-python which I will attempt to resolve by contacting the maintainers of that package):

pip install PyQt5
pip install Biopython
pip install sortedcontainers
pip install bx-python # <-- currently seeing an error here; this is as far as I've got

Note: this was found for both a python3.6 virtualenv I'd created for this work, and a python3 one.

[emzodls]

Thanks, I'll work on this. So bx isn't exactly python 3 compatible and I ran into issues with it in a windows set up. If you pull the "intervaltree" branch of clusterTools it uses the intervaltree package which has better compatibility. Sorry you keep running into all these issues, no one's tried to run the program from the source code before so I haven't really made instructions on how to run it.

[olisteadman]

Thanks @emzodls, having pulled the intervaltree branch and commented out line 30 of clusterAnalysis.py I can confirm this was the finalised list of packages that had to be installed:

pip install PyQt5
pip install Biopython
pip install sortedcontainers
# pip install bx-python # <-- not needed; see previous comments in this GitHub thread
pip install bs4
pip install wget

Having installed them, running python main.py successfully opened the application and I was able to begin following the Manual. thanks for your help with this; looking forward to a requirements.txt so other users can more easily get going but, in the meantime, they should be fine so long as they follow the commands above.