On Jun 28, 2011 4:43 PM, "Nate Coraor" <nate@bx.psu.edu> wrote:
> 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
>> psql (8.4.8)
>> Type "help" for help.
>>
>> galaxy=> \l
>> List of databases
>> Name | Owner | Encoding | Collation | Ctype | Access
>> privileges
>> --------------+----------+----------+------------+------------+-----------------------
>> galaxy | postgres | UTF8 | en_US.utf8 | en_US.utf8 | =Tc/postgres
>> :
>> postgres=CTc/postgres
>> :
>> galaxy=CTc/postgres
>> postgres | postgres | UTF8 | en_US.utf8 | en_US.utf8 |
>> template0 | postgres | UTF8 | en_US.utf8 | en_US.utf8 | =c/postgres
>> :
>> postgres=CTc/postgres
>> template1 | postgres | UTF8 | en_US.utf8 | en_US.utf8 | =c/postgres
>> :
>> postgres=CTc/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):
> ...
>> File
>> "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/strategies.py",
>> 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
>
> Hi Gus,
>
> 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
> universe_wsgi.ini:
>
> postgres:///galaxy?host=/var/run/postgresql
>
> 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;
>
> --nate
>
>>
>>
>> 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: dunnw@uci.edu
>> Email: wadunn83@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*
>
>> ___________________________________________________________
>> Please keep all replies on the list by using "reply all"
>> in your mail client. To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>
>> http://lists.bx.psu.edu/
>