Closed ahratul closed 1 year ago
Hi @ahratul,
Sorry if it wasn't clear enough in the documentation.
The command should be run /<Full/Path/To/Your/Fiji/Dir>/ImageJ-linux64
and then the rest of the command.
To run it - both FIJI and the RS-FISH package should first be installed.
For further questions, please attach the output from check.log and the terminal. Best, Ella
@bellonet ,may i ask you how to run this command as a bash command.
It is a bash command that can be run from the terminal. But you do have a small mistake there, so use this template instead:
<fiji_dir_path>/ImageJ-linux64 --headless --run </path/to/this/script>/RS_macro.ijm &> </path/to/where/you/want/yourlogfile>.log
Notice that everything inside a <> should be edited to the path on the machine you're running it on.
Also notice that &>
should be kept as is (don't delete > there)
Example command:
/home/ella/work/Fiji.app/ImageJ-linux64 --headless --run /home/ella/work/FISH_project/RS_macro_script.ijm &> /home/ella/work/FISH_project/RS_macro_script.log
The full documentation can be found here: https://github.com/PreibischLab/RS-FISH/tree/master/documents/example_scripts
Thank you very much for your message but i am getting this log file
@bellonet i changed the command to this "/home/devasc/Downloads/Fiji.app/ImageJ-linux64 --headless --run /home/devasc/RS_macro.ijm &> /home/devasc/new/check.log"
Please correct /home/devascRS_macro.ijm
to /home/devasc/RS_macro.ijm
and run again.
The run command couldn't find the path that was given.
Thank you very much it worked
Awesome.
Hi can you help me how to run this " ./ImageJ-linux64 --headless --run /home/user/Downloads/fiji-linux64/Fiji.app/scripts//RS_macro.ijm & /home/user/Downloads/check.log" as a bash command