search

drieslab / Giotto

Spatial omics analysis toolbox
https://drieslab.github.io/Giotto_website/
Other
258 stars 98 forks source link

Error in installGiottoEnvironment #309

Closed vwtlin closed 1 year ago

vwtlin commented 2 years ago

Hi Giotto team, thanks for developing such an amazing tool for spatial data. I would like to use it to analyse the ligand receptor interaction but I could not install it properly. I will be grateful if you could provide some help.

I ran this code but having an error:

giotto environment found at /home/cph/.local/share/r-miniconda/envs/giottoenv/bin/python /tmp/RtmpI3W0nT/filed7f970edaae.sh:4:/home/cph/anaconda3/envs/giotto_env/etc/conda/deactivate.d/deactivate-r-base.sh:[[:notfound /tmp/RtmpI3W0nT/filed7f970edaae.sh:5:/home/cph/anaconda3/envs/giotto_env/etc/conda/deactivate.d/deactivate-gxx_linux-64.sh:Syntaxerror:"("unexpected Error in Sys.setenv(PATH = new _path) : wrong length for argument In addition: Warning message: In system2(Sys.which("sh"), fi, stdout = if (identical(intern, FALSE)) ' else intern) running command "'/usr/bin/sh'/tmp/RtmpI3W0nT/filed7f970edaae.sh'had status 2

RubD commented 1 year ago

Did you use the installGiottoEnvironment? I'm also tagging @mattobny here who has been streamlining this process lately.

mattobny commented 1 year ago

Hello @vwtlin, installGiottoEnvironment has undergone some breaking changes over the past few weeks. Please try to run installGiottoEnvironment(force_environment = TRUE, force_miniconda = TRUE); this should remove the old installation and reinstall the environment with the proper specs.

vwtlin commented 1 year ago

Hi @RubD @mattobny Thanks very much for your help. After following the updated tutorial, which is more clear to me, I was able to install the python environment manually and assign my python to Gitto. Everything is working now.

Cheers, Weitao