Hi Rob,
Indeed, I had/have some difficulties with setting temporary
directories. The problem was that FTP uploaded data was first copied to
TMPDIR prior to being put in the database directory.
My solution: I extended the /tmp partition to several GB's, by mounting
a bigger device over it.
Joachim, Nate,
Leon Mei pointed me to a mailing list post of August 2012 where you two
discussed a problem with uploads to Galaxy filling up /tmp. I think I have
traced this down now after we suffered from this too several times.
There are a number of places where temporary files are
Hi Nate,
I have set the new_file_path to the FTP upload directory as you
suggested. new_file_path=/mnt/galaxydb/ftp
This did not succeed however: still there is copying to the /tmp directory.
I also see that importing data sets into data libraries from a directory
of files behaves
On Aug 17, 2012, at 3:17 AM, Joachim Jacob wrote:
Hi Nate,
thanks. Do you know what's the reason for using copying first the contents to
the /tmp directory, before copying it into a the database/files/... Seems
inefficient to do so, or is this not how it works perhaps?
Hi Joachim,
If
Hi Nate,
thanks. Do you know what's the reason for using copying first the
contents to the /tmp directory, before copying it into a the
database/files/... Seems inefficient to do so, or is this not how it
works perhaps?
Regards,
Joachim
Joachim Jacob, PhD
Rijvisschestraat 120, 9052
Excuses for the repost, but I really need to solve this.
Uploading with FTP fails on our Galaxy, because the /tmp directory has
not enough space. How can I hack in the Galaxy code base that the
temporary directory needs to be /mnt/galaxydb/tmp ? Another solution:
how can I provide a symlink
On Aug 16, 2012, at 11:09 AM, Joachim Jacob wrote:
Excuses for the repost, but I really need to solve this.
Uploading with FTP fails on our Galaxy, because the /tmp directory has not
enough space. How can I hack in the Galaxy code base that the temporary
directory needs to be
Dear devs,
Question about FTP upload: is it correct that Galaxy copies the data
from the FTP upload directory to galaxy database instead of symlinking?
Can I set somewhere the option to symlink instead of copying?
I run galaxy in a small virtual machine. The Galaxy database is on a
network
