search

OBOAcademy / obook

OBO Organized Knowledge: Training materials for becoming an OBO engineer
https://oboacademy.github.io/obook/
Creative Commons Zero v1.0 Universal
91 stars 38 forks source link

Simple 5 step installation guide for Protege 5.6.1 #363

Closed matentzn closed 1 year ago

rays22 commented 1 year ago

5 step installation guide for Protégé

  1. Click here to find latest release of Protégé. Choose and download the appropriate files for your operating system (Linux, macOS, Windows, platform independent).
  2. Use the PGP signature contained in the appropriate file with an .asc extension to verify the integrity of the downloaded Protégé version.
  3. Decompress the downloaded .zip or .tar.gz file with tools appropriate for your operating system.
  4. Follow the steps as needed by your operating system to install the Protégé application. For example, on macOS: drag and drop Protégé.app to the Applications folder and replace any older versions of the software. You may need to right click Protégé.app and then choose Open from the menu to authorise the programme to run on your machine.
  5. Adjust memory settings if necessary. Memory settings can now be adjusted in a jvm.conf configuration file that can be located either in the .protege/conf directory under your home directory, or in the conf directory within the application bundle itself. For example, to set the maximum amount of memory available for Protégé to, say, 12GB, put the following in the jvm.conf file: 
    max_heap_size=12G
    • On macOS, you can find the file is here:
/Applications/Protégé.app/Contents/conf/jvm.conf

Edit this part:

# Uncomment the line below to set the maximal heap size to 8G
#max_heap_size=8G
matentzn commented 1 year ago

@rays22 THANK you the hardest part was to figure out how to give permission on a Mac..

Go to Preferences -> Security -> General

You need to open the little lock, then click "Mac stopped an application from Running (Protege)" -> Open anyways

rays22 commented 1 year ago

If I right click on Protege.app in Applications the first time, then it gives a severe warning about security risks, but there is a choice to Open. I click 'Open' and it does open. Subsequently it opens without any warning or problem.

Shall I put this document to obook/docs)/howto/?

balhoff commented 1 year ago

I'm working on the GO editors guide; I have a couple useful screenshots here for allowing it to run: https://wiki.geneontology.org/Protege5_6_setup_for_GO_Eds#Download_and_install_Protege