Hi all,
Just to share some experiences about temporary directories.
- System /tmp is best put on a separate partition, with nosuid and noexec set. In /etc/fstab for example UUID=e35e1...d3 /tmp ext4 noexec,nosuid,noatime,nodiratime 0 0 - /tmp needs to be big, because it is used as temporarily storage for FTP upload to your galaxy (and copying from data libraries) - If you set the /tmp as described above, installation of R packages might be not working. /tmp is being used here by default, and no execution is allowed (noexec). If you encounter this, set env variable TMPDIR to some directory with exec perms: export TMPDIR='/var/tmp' before trying installation of R packages. - Of course, Galaxy has it's own temporary directory, set in universe_wsgi.ini as new_file_path (e.g. new_file_path = /mnt/galaxytemp). This is mainly used for tools needing temporary space. However, note that not all tools use this temporary directory, and use the system default. If designing tools however, it is best to pass ${__new_file_path__} in the cheetah template of your tool's xml to the tool, to allow using the Galaxy temporary directory.
My 2 cents... if somebody want to add something, please do.
Joachim