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*
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