Optional "gsea_home" directory

[bounlu]

By default, gsea-cli sets "gsea_home" to user's HOME directory to write some cache files. Is there an option to set this to another directory when running the gsea-cli?

[davideby]

@bounlu Sorry, that isn't exposed as a settable preference. It is possible to redirect the report output directories from HOME/gsea_home/output to a different location. It needs to be done in the UI through File > Preferences > General > Report settings rather than through gsea-cli, but it should remain in effect after being set.

That might not be enough to accomplish what you want, though, since GSEA Desktop creates certain other files in gsea_home. Unfortunately it's hard to change that, but let's keep this issue open as a feature request and I'll see what we can do to accommodate it. To be clear, would it be enough to move the cache files elsewhere? It's very handy to have a fixed location for certain things like log files.

Having said all of that, it is possible to do if you are willing to change the user.home property setting for Java. That is, you would be telling the JVM that runs GSEA that the HOME is elsewhere. GSEA always creates this directory in HOME/gsea_home, so this might accomplish what you need.

The problem there is that it might cause problems with things like relative file paths. You ought to be able to work around that with explicit absolute paths, though. If you try it, let us know how it goes.

[davideby]

Here's a (very old) StackOverflow thread that show how one might go about setting user.home:
https://stackoverflow.com/questions/1501235/change-user-home-system-property