W. Augustine Dunn III wrote:
> Hello all:
> Please forgive me if this is a matter of RTFM but I can assure you that I
> have in fact TRIED that for a day or so now...
> I am trying to set up a local GALAXY site for my lab so that I can start to
> offload some of the work that comes my way as the sole biologist in our lab
> not afraid of the command line. My system is Ubuntu 10.10 64b, i7 quad, 12
> GB RAM. Since Multiple people will be using the site I decided to go with
> the slightly more fancy postgresql db back-end rather than the sqlite
> default. I had things running fine with the sqlite but can NOT seem to get
> psql and galaxy to play nice.
> I have created a galaxy role with rights to make tables on a created
> "galaxy" database:
> galaxy@vlad 12:40:20 ~/galaxy-dist:
> psql (8.4.8)
> Type "help" for help.
> galaxy=> \l
> List of databases
> Name | Owner | Encoding | Collation | Ctype | Access
> galaxy | postgres | UTF8 | en_US.utf8 | en_US.utf8 | =Tc/postgres
> postgres | postgres | UTF8 | en_US.utf8 | en_US.utf8 |
> template0 | postgres | UTF8 | en_US.utf8 | en_US.utf8 | =c/postgres
> template1 | postgres | UTF8 | en_US.utf8 | en_US.utf8 | =c/postgres
> zabbix_proxy | postgres | UTF8 | en_US.utf8 | en_US.utf8 |
> (5 rows)
> I created a PGDATA file at /var/lib/postgresql/8.4/main/PGDATA and export a
> PGDATA envar upon loading of the galaxy user's .bashrc pointing to this
> place. I am able to start and stop the server with the postgres user using
> pg_ctl. Once its running, I change users back to galaxy and try to run
> run.sh and get the following traceback:
> Traceback (most recent call last):
> line 80, in connect
> raise exc.DBAPIError.instance(None, None, e)
> OperationalError: (OperationalError) could not connect to server: No such
> file or directory
> Is the server running locally and accepting
> connections on Unix domain socket "/tmp/.s.PGSQL.5432"?
> None None
The version of PostgreSQL bundled with Debian and its derivatives
(including Ubuntu) places the UNIX socket used by local processes for
communication with PostgreSQL in /var/run/postgresql. You can instruct
Galaxy to look here with the following database_connection string in
Also, unless I'm missing something, it looks like your galaxy role would
not have permissions o nthat database (perms are only assigned to the
postgres role). The easiest fix would be to make galaxy the owner of
the galaxy database:
ALTER DATABASE galaxy OWNER TO galaxy;
> I have reached the point where I am beating my head against a wall and
> finally decided to ask for help. I am probably not as experienced as a pure
> compSci person but i have been hacking python/bash/perl for years. However
> I am not experienced at ALL with SQL flavors.
> I hope that this give someone enough info to be able to help me! Again I am
> sorry if this has been addressed already. I searched the archives but came
> up with nothing.
> Thanks in advance!
> Gus Dunn
> Molecular Biology and Biochemistry
> Institute for Genomics and Bioinformatics
> Major Advisor: Anthony James
> Co-Advisor: Xiaohui Xie
> University of California, Irvine
> 2315 McGaugh Hall
> Irvine, CA 92697-3900
> Lab: (949) 824-3210
> Fax: (949) 824-8551
> Email: du...@uci.edu
> Email: wadun...@gmail.com
> In science, "fact" can only mean "confirmed to such a degree that it would
> be perverse to withhold provisional assent." I suppose that apples might
> start to rise tomorrow, but the possibility does not merit equal time in
> physics classrooms.
> *-Stephen Jay Gould*
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