Scaffold DIA, PTM, LFQ, and Elements
To troubleshoot or specify a different temporary directory in a toolkit-based product, eg, Scaffold DIA, you can launch it like so:
/path/to/ScaffoldDIA -J-Djava.io.tmpdir=/path/to/new/scaffolddia/tmp/
This should work for all our products except Scaffold 5 and Scaffold Q+S.
Scaffold 5/Q+S/Batch
Multiple instances sharing the same temp file can cause problems when running simultaneous Scaffold Batch runs. Here is an idea to work around this:
https://stackoverflow.com/questions/1924136/environment-variable-to-control-java-io-tmpdir
You can set your JVM settings before running the job to use different temp space, eg:
/tmp/sfd_batch_<uuid>
Scaffold has no built-in way to configure this, but if you are running from the command line, you might be able to do this with Python or bash:
export _JAVA_OPTIONS=-Djava.io.tmpdir=/new/tmp/dir
On Windows, you can open the cmd.exe and run the following command:
set _JAVA_OPTIONS=-Djava.io.tmpdir=D:\new\tmp\dir
Then run Scaffold from the command line:
C:\Program Files\Scaffold\Scaffold.exe
This should start using the temp path you set above for this instance of Scaffold.