search

Becksteinlab / GromacsWrapper

GromacsWrapper wraps system calls to GROMACS tools into thin Python classes (GROMACS 4.6.5 - 2024 supported).
https://gromacswrapper.readthedocs.org
GNU General Public License v3.0
169 stars 53 forks source link

get_GMXRC fails on macOS with brew #148

Closed richardjgowers closed 3 years ago

richardjgowers commented 6 years ago

So I'm trying out a "new user experience" and trying to install this from scratch. So on MacOS there's no conda package for gromacs 2018, so I used brew.

I get this failure: def test_set_gmxrc_environment():

(gromacs) [~/code/GromacsWrapper]> which gmx /usr/local/bin/gmx

Whereas my GMXRC is at: /usr/local/share/GMXRC

It looks like the code looks in GMXRC = os.path.join(bindir, 'GMXRC')

I'm not entirely sure how installation "usually" works, but is it worth adding the ../share/ location too?

orbeckst commented 6 years ago

I'd say brew is installing in the wrong place. A standard Gromacs installation always places it in bin.

orbeckst commented 6 years ago

We could add code (with a comment about weird brew installations...) to catch it. Make a PR.

(I don't use brew. Not sure where Macports installs Gromacs, if it is even present.)

orbeckst commented 6 years ago

Btw, please just ping me if there's no reply in a day or two – I only see issues when I check various GitHub dashboards and there's not always time in the day available for indulging in such activity.

richardjgowers commented 6 years ago

Yeah so maybe brew is wrong, but I do think we should cater for people that lazily install gromacs like me :) I'll do a fix

orbeckst commented 3 years ago

Just for anyone looking here: bioconda has macOS GROMACS packages for 2018, 2019, 2020, 2021 https://anaconda.org/bioconda/gromacs/files (although for serious work I'd still compile my own).

I am not sure if the issue with brew persists. I'll tentatively mark this as won't fix but if anyone still considers it a problem please add your voice here and we can reopen.