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dipetkov / eems

Estimating Effective Migration Surfaces
GNU General Public License v2.0
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Pipeline requires more libraries #22

Closed YanisChrys closed 6 years ago

YanisChrys commented 6 years ago

Hello, I am using EEMS in a server where I don't have sudo priviledges and it turns out EEMS needs more libraries than you say in the readme. When I tried running it it also couldn't find fiona, collections, mpl_toolkit and descartes along with pandas and shapely. Could you add those to the list of needed packages?

BenjaminPeter commented 6 years ago

hi John,

these are dependencies on some python stuff I pushed to the repo to make stuff a bit easier, but they are not needed to run eems (and probably not functional). Just use the bed2diffs and runeems executables directly. Desi, you probably should delete the pipeline folder as it is not used.

On Sat, Feb 10, 2018 at 9:31 PM, JohnChrys notifications@github.com wrote:

Hello, I am using EEMS in a server where I don't have sudo priviledges and it turns out EEMS needs more libraries than you say in the readme. When I tried running it it also couldn't find fiona, collections, mpl_toolkit and descartes along with pandas and shapely. Could you add those to the list of needed packages?

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YanisChrys commented 6 years ago

Hi Mr Peter, Thank you for your reply. Even though they're not needed to run it, when I do python pipeline_cli.py -h upon not detecting those packages on the server it fails and outputs an error message. I haven't tried running the pipeline per se, but I imagine failing to load these libraries would cause the run to fail as it does for the -h command.

I am now trying to use the bed2diffs and runeems executables, yes. If they're the only ones worth running right now, you could always make a vignette for them and/or the best way of running them that works for you.

John

meisei4 commented 2 weeks ago

Is there any plans for this pipeline to be updated to work with modern package versions?