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/lib/galaxy/web/buildapp.py", line 82, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/home/galaxy/galaxy-dist/lib/galaxy/app.py", line 32, in __init__ create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options ) File "/home/galaxy/galaxy-dist/lib/galaxy/model/migrate/check.py", line 54, in create_or_verify_database dataset_table = Table( "dataset", meta, autoload=True ) File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/schema.py", line 108, in __call__ return type.__call__(self, name, metadata, *args, **kwargs) File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/schema.py", line 236, in __init__ _bind_or_error(metadata).reflecttable(self, include_columns=include_columns) File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 1261, in reflecttable conn = self.contextual_connect() File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/threadlocal.py", line 194, in contextual_connect return self.session.get_connection(**kwargs) File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/threadlocal.py", line 20, in get_connection return self.engine.TLConnection(self, self.engine.pool.connect(), close_with_result=close_with_result) File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/pool.py", line 151, in connect agent = _ConnectionFairy(self) File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/pool.py", line 304, in __init__ rec = self._connection_record = pool.get() File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/pool.py", line 161, in get return self.do_get() File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/pool.py", line 639, in do_get con = self.create_connection() File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/pool.py", line 122, in create_connection return _ConnectionRecord(self) File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/pool.py", line 198, in __init__ self.connection = self.__connect() File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/pool.py", line 261, in __connect connection = self.__pool._creator() 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
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
Hi Gus, it seems that your postgres is not configured to accept connection except localhost (or the deamon is not running). Did you try to connect to postgres from another PC in the network (no the localhost)? Did you install postgres using apt-get install? Do you run postgres using "/etc/init.d/postgresql-8.4 start"? Greets.
--- Marco
On 24 June 2011 21:52, W. Augustine Dunn III wadunn83@gmail.com 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/lib/galaxy/web/buildapp.py", line 82, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/home/galaxy/galaxy-dist/lib/galaxy/app.py", line 32, in __init__ create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options ) File "/home/galaxy/galaxy-dist/lib/galaxy/model/migrate/check.py", line 54, in create_or_verify_database dataset_table = Table( "dataset", meta, autoload=True ) File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/schema.py", line 108, in __call__ return type.__call__(self, name, metadata, *args, **kwargs) File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/schema.py", line 236, in __init__ _bind_or_error(metadata).reflecttable(self, include_columns=include_columns) File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 1261, in reflecttable conn = self.contextual_connect() File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/threadlocal.py", line 194, in contextual_connect return self.session.get_connection(**kwargs) File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/threadlocal.py", line 20, in get_connection return self.engine.TLConnection(self, self.engine.pool.connect(), close_with_result=close_with_result) File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/pool.py", line 151, in connect agent = _ConnectionFairy(self) File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/pool.py", line 304, in __init__ rec = self._connection_record = pool.get() File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/pool.py", line 161, in get return self.do_get() File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/pool.py", line 639, in do_get con = self.create_connection() File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/pool.py", line 122, in create_connection return _ConnectionRecord(self) File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/pool.py", line 198, in __init__ self.connection = self.__connect() File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/pool.py", line 261, in __connect connection = self.__pool._creator() 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
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:
Hi,
Could you please show us the contents of your pg_hba.conf file? This is where you configure which machines can access the database through the network.
Best, L-A
Le 27/06/2011 20:33, Marco Moretto a écrit :
Hi Gus, it seems that your postgres is not configured to accept connection except localhost (or the deamon is not running). Did you try to connect to postgres from another PC in the network (no the localhost)? Did you install postgres using apt-get install? Do you run postgres using "/etc/init.d/postgresql-8.4 start"? Greets.
Marco
On 24 June 2011 21:52, W. Augustine Dunn III <wadunn83@gmail.com mailto:wadunn83@gmail.com> 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/lib/galaxy/web/buildapp.py", line 82, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/home/galaxy/galaxy-dist/lib/galaxy/app.py", line 32, in __init__ create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options ) File "/home/galaxy/galaxy-dist/lib/galaxy/model/migrate/check.py", line 54, in create_or_verify_database dataset_table = Table( "dataset", meta, autoload=True ) File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/schema.py", line 108, in __call__ return type.__call__(self, name, metadata, *args, **kwargs) File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/schema.py", line 236, in __init__ _bind_or_error(metadata).reflecttable(self, include_columns=include_columns) File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 1261, in reflecttable conn = self.contextual_connect() File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/threadlocal.py", line 194, in contextual_connect return self.session.get_connection(**kwargs) File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/threadlocal.py", line 20, in get_connection return self.engine.TLConnection(self, self.engine.pool.connect(), close_with_result=close_with_result) File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/pool.py", line 151, in connect agent = _ConnectionFairy(self) File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/pool.py", line 304, in __init__ rec = self._connection_record = pool.get() File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/pool.py", line 161, in get return self.do_get() File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/pool.py", line 639, in do_get con = self.create_connection() File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/pool.py", line 122, in create_connection return _ConnectionRecord(self) File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/pool.py", line 198, in __init__ self.connection = self.__connect() File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/pool.py", line 261, in __connect connection = self.__pool._creator() 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 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 <mailto:dunnw@uci.edu> Email:wadunn83@gmail.com <mailto: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/
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:
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:
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" 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*
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Louise-Amélie Schmitt -
Marco Moretto -
Nate Coraor -
W. Augustine Dunn III