Changing Temp Space For Each Scaffold Instance

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 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