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labsyspharm / basic-illumination

ImageJ BaSiC shading correction for use with Ashlar
MIT License
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"ImageJ: command not found" on Galaxy #7

Closed hengkp closed 1 year ago

hengkp commented 2 years ago

Hi Developers,

I am first experiencing the Galaxy. I tried to run BaSiC Illumination in Galaxy, which was installed on macOS Monterey version 12.5. It showed an error as ".../tool_script.sh: line 26: ImageJ: command not found". Please kindly helps on this issue.

Thanks, Heng

alliecreason commented 2 years ago

Hi Heng,

Could you tell us a bit more about your galaxy set up. Is this a local installation of galaxy? Has it been configured for running tools in conda environments or docker containers?

hengkp commented 2 years ago

Hi @alliecreason,

Thank you for your reply. I installed galaxy locally under the "/Users/heng/galaxy" directory. Also, conda and docker are available in the base environment (the version shown below).

Screen Shot 2565-07-30 at 09 29 39

Apart from the installation of galaxy followed by this page, I have only set an admin user and installed tools in the galaxy. It might not be configured either conda or docker yet. So, which one should I select to run your workflow perfectly?

Thanks, Heng

Xujingkk commented 1 year ago

Hi @hengkp, I had the same problem as you, have you solved it now? Can you tell me how it was solved? Thanks a lot

hengkp commented 1 year ago

Hi @Xujingkk ,

Unfortunately, I did not solve this problem. I have been moving to the MCMICRO which contains the BaSiC package as an optional tool according to the reference here. There is also a Galaxy version that you can try, but I recommend using the command's version.

Hope this helps, Heng