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 you set new_file_path in universe_wsgi.ini to be on the same filesystem as your FTP upload directory, there should not be any copying necessary. Thanks, --nate > > 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 >>>> >>> ___________________________________________________________ >>> 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/ > ___________________________________________________________ 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/
