Thanks Dannon, I indeed managed to have the galaxy-central version installed. I already see some problems but I will open another thread if necessary. Regards the DB engine, this new Galaxy I am deploying now is only a toy server I want to use in the Galaxy meeting in Oslo. I would like to have the same configuration as the other server we already have which using MySQL. Thx a lot for your help JF On 06/21/2013 11:26 AM, Dannon Baker wrote:
Hi Jean-François,
The index issues preventing a new instance from starting are resolved in the stable branch of galaxy-central; if you pull updates from that branch you should be able to start a new instance. While the instance will start and run, there are other peculiarities I still need to resolve and I'd really recommend using postgres for a new instance at this time if you're at all able to do so.
-Dannon
On Fri, Jun 21, 2013 at 5:07 AM, jean-François Taly <jean-francois.taly@crg.eu <mailto:jean-francois.taly@crg.eu>> wrote:
Dear all,
I am having the same problem as Linda with a fresh installation of version 20130603. In the thread of her mail Dannon Baker said :
"That said, this doesn't resolve the mysql index issues, which I'm currently working on. I hope to have a fix for them available soon, though."
I would like to know if what is the status of this thread. Should I use the solution provided in Linda's mail (CREATE INDEX ix_history_slug ON history (slug(1000));)
Thx a lot for your help
Best
Jean-François
On 06/05/2013 05:12 PM, Linda Cham wrote:
Hi. I am new to the Galaxy forum and I am trying to setup a new local Galaxy instance with MySQL on RH6.2 x86_64.
On a newly installed OS node, using the hg clone command (hg clone _https://bitbucket.org/galaxy/galaxy-dist#stable_ <https://bitbucket.org/galaxy/galaxy-dist>) which gets the current Galaxy 20130603 image, I am getting the following errors when running run.sh: File "build/bdist.linux-x86_64-ucs4/egg/MySQLdb/cursors.py", line 173, in execute self.errorhandler(self, exc, value) File "build/bdist.linux-x86_64-ucs4/egg/MySQLdb/connections.py", line 36, in defaulterrorhandler raise errorclass, errorvalue OperationalError: (OperationalError) (1170, "BLOB/TEXT column 'slug' used in key specification without a key length") 'CREATE INDEX ix_history_slug ON history (slug)' ()
Reading the forum, someone stated it can be bypass by running the CREATE INDEX.
mysql> CREATE INDEX ix_history_slug ON history (slug(1000)); Query OK, 0 rows affected (0.09 sec) Records: 0 Duplicates: 0 Warnings: 0
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-- ##################################### Jean-François Taly Bioinformatician Bioinformatics Core Facility http://biocore.crg.cat CRG - Centre de Regulació Genòmica (Room 439) Parc de Recerca Biomèdica de Barcelona (PRBB) Doctor Aiguader, 88 08003 Barcelona Spain email:jean-francois.taly@crg.eu phone: +34 93 316 0202 fax: +34 93 316 0099 #####################################