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 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib

On 08/16/2012 05:19 PM, Nate Coraor wrote:
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 /mnt/galaxydb/tmp ? Another solution: how can I provide a 
symlink to our FTP directory?
Hi Joachim,

It's not possible with the FTP upload method, but if you set user_library_import_dir in 
the config file, users can upload files from a server directory and choose the 
"link" option, just like an admin can.

--nate


Thanks for any hint,

Joachim


Joachim Jacob, PhD

Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib

On 08/08/2012 12:12 PM, Joachim Jacob wrote:
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 
share. With 'get data' - 'Upload file', when importing the files I have 
uploaded with FTP, there is a process filling up the /tmp directory with the 
file I want to import.


Kind regards,
Joachim

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