On 11/02/2012 02:20 PM, Vladimir Yamshchikov wrote:
Someone has advised also that SQLite, which is the default option,
> is not adequate for serious work. Is this something I need to
> change too?

Indeed, see:
http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server


> I mean could this prevent dataset upload? I tried to intall
> PostgreSQL, but it is quite messy and instructions are far
> from beng adequate or even accurate.

Although, using SQLite has many disadvantages, I doubt, it has a direct influence on the actual upload process.

Well, it has been a while since I last installed PostgreSQL from scratch, but I never ran into troubles. And since PostgreSQL is an Open Source Project as well, there is a lot of support available, see:
http://www.postgresql.org/community/


Regards, Hans-Rudolf




Vladimir

----- Original Message -----
From: "Hans-Rudolf Hotz" <h...@fmi.ch>
To: "Vladimir Yamshchikov" <yaxi...@gmail.com>
Cc: <galaxy-dev@lists.bx.psu.edu>
Sent: Thursday, November 01, 2012 3:18 AM
Subject: Re: [galaxy-dev] Dataset upload fail


Hi Vladimir

On 11/01/2012 03:46 AM, Vladimir Yamshchikov wrote:
Local install of Galaxy on SciLinux55. Fails to upload 5.2 GB fastq file
from local HD, while normally loading smaller fastq and fasta datasets
(less than 1 GB). Chunks of 1.2 GB size remain in */database/tmp, which
all represent beginning of the file that fails to upload. Several
attempts to upload made and several chunks of the same size are present.
Can I just copy the file dataset to database directory instead of
uploading through web interface?



Make sure you provide a directory for "library_import_dir" in the
universe_wsgi.ini file.  And copy your files to this location (or a sub
directory of it). This will give you an extra option in the admin menu:
'Upload directory of files' and then use the 'Link files without copying
to Galaxy' option.


Alternatively, set "allow_library_path_paste" to 'True' (see also the
comments and warnings in the universe_wsgi.ini file )


Regards, Hans-Rudolf










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