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" <hrh@fmi.ch> To: "Vladimir Yamshchikov" <yaximik@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