Thanks every one. I am in Bethesda for a conference at the moment, but I will try your suggestions when I get back home.
Gus Sent from my HTC EVO. Please forgive any typos and/or brevity of my reply. On Jun 28, 2011 4:43 PM, "Nate Coraor" <n...@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: 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* > >> ___________________________________________________________ >> 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/ >
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