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
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:
----- Original Message -----
From: "Hans-Rudolf Hotz" <hrh(a)fmi.ch>
To: "Vladimir Yamshchikov" <yaximik(a)gmail.com>
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
> comments and warnings in the universe_wsgi.ini file )
> Regards, Hans-Rudolf