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