Run this command as bash command

[ahratul]

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

[bellonet]

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

[ahratul]

@bellonet ,may i ask you how to run this command as a bash command.

[bellonet]

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

[ahratul]

Thank you very much for your message but i am getting this log file

[ahratul]

@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"

[bellonet]

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.

[ahratul]

Thank you very much it worked

[bellonet]

Awesome.