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
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
