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3dem / relion

Image-processing software for cryo-electron microscopy
https://relion.readthedocs.io/en/latest/
GNU General Public License v2.0
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Relion/5.0b does not acknowledge variable for cryoCARE executable path #1130

Open yangr3 opened 1 month ago

yangr3 commented 1 month ago

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Describe your problem

Hello, we installed cryoCARE and Relion/5.0b on the cluster, set cryoCARE executable environment in the lmod module file together with other external executable like AreTomo: setenv("RELION_AreTomo_EXECUTABLE", "AreTomo") setenv("RELION_cryoCARE_EXECUTABLE", "/usr/local/apps/cryocare/0.3.0/bin/")

Relion5 GUI will acknowledge the AreTomo setting bot not cryoCARE, the directory with cryoCARE executables is still default: "/public/EM/cryoCARE" It looks like the variable is not set in Relion5.

Thanks for looking into this.

DanGonite57 commented 1 month ago

Hello, the RELION GUI itself has a field where the cryoCARE directory can be changed (the field is filled with /public/EM/cryoCARE by default). Does changing this field not work for you?

yangr3 commented 1 month ago

Hello Daniel, thanks for the reply. Changing path in the Relion/5.0b GUI will allow the executable being correctly pointed. But I had to email users whenever they ran into issue for that. It would be ideal if we could change/define the default path of that variable just like it is allowed for other external apps such as AreTomo. Thanks.