It looks like you don't have you postgres database set up correctly to accept communication.  Check the postgres documentation.

On Oct 21, 2011, at 1:54 AM, Luciano Cosme wrote:

Thanks Greg,
   I created the database instance and set the path at universe_wsgi.ini. Then when I run sh run.sh I get the following error message:


root@aedes:/home/koala2/galaxy-dist# sh run.sh
python path is: /home/koala2/galaxy-dist/eggs/numpy-1.6.0-py2.7-linux-x86_64-ucs4.egg, /home/koala2/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs4.egg, /home/koala2/galaxy-dist/eggs/Whoosh-0.3.18-py2.7.egg, /home/koala2/galaxy-dist/eggs/pycrypto-2.0.1-py2.7-linux-x86_64-ucs4.egg, /home/koala2/galaxy-dist/eggs/python_lzo-1.08_2.03_static-py2.7-linux-x86_64-ucs4.egg, /home/koala2/galaxy-dist/eggs/bx_python-0.7.0_494c2d1d68b3_rebuild1-py2.7-linux-x86_64-ucs4.egg, /home/koala2/galaxy-dist/eggs/amqplib-0.6.1-py2.7.egg, /home/koala2/galaxy-dist/eggs/pexpect-2.4-py2.7.egg, /home/koala2/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg, /home/koala2/galaxy-dist/eggs/Babel-0.9.4-py2.7.egg, /home/koala2/galaxy-dist/eggs/MarkupSafe-0.12-py2.7-linux-x86_64-ucs4.egg, /home/koala2/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg, /home/koala2/galaxy-dist/eggs/WebHelpers-0.2-py2.7.egg, /home/koala2/galaxy-dist/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs4.egg, /home/koala2/galaxy-dist/eggs/wchartype-0.1-py2.7.egg, /home/koala2/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg, /home/koala2/galaxy-dist/eggs/docutils-0.7-py2.7.egg, /home/koala2/galaxy-dist/eggs/WebOb-0.8.5-py2.7.egg, /home/koala2/galaxy-dist/eggs/Routes-1.12.3-py2.7.egg, /home/koala2/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg, /home/koala2/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg, /home/koala2/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg, /home/koala2/galaxy-dist/eggs/Paste-1.6-py2.7.egg, /home/koala2/galaxy-dist/lib, /usr/lib/python2.7, /usr/lib/python2.7/plat-linux2, /usr/lib/python2.7/lib-tk, /usr/lib/python2.7/lib-old, /usr/lib/python2.7/lib-dynload, /usr/local/lib/python2.7/dist-packages, /usr/lib/python2.7/dist-packages/PIL, /usr/lib/python2.7/dist-packages/gst-0.10, /usr/lib/python2.7/dist-packages/gtk-2.0, /usr/lib/pymodules/python2.7, /usr/lib/python2.7/dist-packages/ubuntu-sso-client, /usr/lib/python2.7/dist-packages/ubuntuone-client, /usr/lib/python2.7/dist-packages/ubuntuone-control-panel, /usr/lib/python2.7/dist-packages/ubuntuone-couch, /usr/lib/python2.7/dist-packages/ubuntuone-installer, /usr/lib/python2.7/dist-packages/ubuntuone-storage-protocol, /usr/lib/python2.7/dist-packages
galaxy.datatypes.registry DEBUG 2011-10-21 00:28:30,646 Loading datatypes from datatypes_conf.xml
galaxy.datatypes.registry DEBUG 2011-10-21 00:28:30,648 Loaded display application 'ucsc_bam' for datatype 'bam', inherit=False
galaxy.datatypes.registry DEBUG 2011-10-21 00:28:30,649 Loaded display application 'ensembl_bam' for datatype 'bam', inherit=False
galaxy.datatypes.registry DEBUG 2011-10-21 00:28:30,649 Loaded display application 'genetrack_interval' for datatype 'bed', inherit=False
galaxy.datatypes.registry DEBUG 2011-10-21 00:28:30,651 Loaded display application 'ucsc_bigbed' for datatype 'bigbed', inherit=False
galaxy.datatypes.registry DEBUG 2011-10-21 00:28:30,653 Loaded display application 'ucsc_bigwig' for datatype 'bigwig', inherit=False
galaxy.datatypes.registry DEBUG 2011-10-21 00:28:30,656 Loaded display application 'ensembl_gff' for datatype 'gff', inherit=True
galaxy.datatypes.registry DEBUG 2011-10-21 00:28:30,657 Loaded display application 'genetrack_interval' for datatype 'interval', inherit=True
galaxy.datatypes.registry DEBUG 2011-10-21 00:28:30,660 Loaded display application 'ensembl_interval' for datatype 'interval', inherit=True
galaxy.datatypes.registry DEBUG 2011-10-21 00:28:30,661 Loaded display application 'gbrowse_interval_as_bed' for datatype 'interval', inherit=True
galaxy.datatypes.registry DEBUG 2011-10-21 00:28:30,664 Loaded display application 'ucsc_maf_customtrack' for datatype 'mafcustomtrack', inherit=False
galaxy.datatypes.assembly DEBUG 2011-10-21 00:28:30,664 Velvet log info  JJ __init__
galaxy.datatypes.registry DEBUG 2011-10-21 00:28:30,669 Loaded sniffer for datatype: galaxy.datatypes.tabular:Vcf
galaxy.datatypes.registry DEBUG 2011-10-21 00:28:30,669 Loaded sniffer for datatype: galaxy.datatypes.binary:TwoBit
galaxy.datatypes.registry DEBUG 2011-10-21 00:28:30,669 Loaded sniffer for datatype: galaxy.datatypes.binary:Bam
galaxy.datatypes.registry DEBUG 2011-10-21 00:28:30,669 Loaded sniffer for datatype: galaxy.datatypes.binary:Sff
galaxy.datatypes.registry DEBUG 2011-10-21 00:28:30,669 Loaded sniffer for datatype: galaxy.datatypes.xml:BlastXml
galaxy.datatypes.registry DEBUG 2011-10-21 00:28:30,669 Loaded sniffer for datatype: galaxy.datatypes.sequence:Maf
galaxy.datatypes.registry DEBUG 2011-10-21 00:28:30,669 Loaded sniffer for datatype: galaxy.datatypes.sequence:Lav
galaxy.datatypes.registry DEBUG 2011-10-21 00:28:30,669 Loaded sniffer for datatype: galaxy.datatypes.sequence:csFasta
galaxy.datatypes.registry DEBUG 2011-10-21 00:28:30,669 Loaded sniffer for datatype: galaxy.datatypes.qualityscore:QualityScoreSOLiD
galaxy.datatypes.registry DEBUG 2011-10-21 00:28:30,669 Loaded sniffer for datatype: galaxy.datatypes.qualityscore:QualityScore454
galaxy.datatypes.registry DEBUG 2011-10-21 00:28:30,670 Loaded sniffer for datatype: galaxy.datatypes.sequence:Fasta
galaxy.datatypes.registry DEBUG 2011-10-21 00:28:30,670 Loaded sniffer for datatype: galaxy.datatypes.sequence:Fastq
galaxy.datatypes.registry DEBUG 2011-10-21 00:28:30,670 Loaded sniffer for datatype: galaxy.datatypes.interval:Wiggle
galaxy.datatypes.registry DEBUG 2011-10-21 00:28:30,670 Loaded sniffer for datatype: galaxy.datatypes.images:Html
galaxy.datatypes.registry DEBUG 2011-10-21 00:28:30,670 Loaded sniffer for datatype: galaxy.datatypes.images:Pdf
galaxy.datatypes.registry DEBUG 2011-10-21 00:28:30,670 Loaded sniffer for datatype: galaxy.datatypes.sequence:Axt
galaxy.datatypes.registry DEBUG 2011-10-21 00:28:30,670 Loaded sniffer for datatype: galaxy.datatypes.interval:Bed
galaxy.datatypes.registry DEBUG 2011-10-21 00:28:30,670 Loaded sniffer for datatype: galaxy.datatypes.interval:CustomTrack
galaxy.datatypes.registry DEBUG 2011-10-21 00:28:30,670 Loaded sniffer for datatype: galaxy.datatypes.interval:Gtf
galaxy.datatypes.registry DEBUG 2011-10-21 00:28:30,670 Loaded sniffer for datatype: galaxy.datatypes.interval:Gff
galaxy.datatypes.registry DEBUG 2011-10-21 00:28:30,670 Loaded sniffer for datatype: galaxy.datatypes.interval:Gff3
galaxy.datatypes.registry DEBUG 2011-10-21 00:28:30,670 Loaded sniffer for datatype: galaxy.datatypes.tabular:Pileup
galaxy.datatypes.registry DEBUG 2011-10-21 00:28:30,670 Loaded sniffer for datatype: galaxy.datatypes.interval:Interval
galaxy.datatypes.registry DEBUG 2011-10-21 00:28:30,670 Loaded sniffer for datatype: galaxy.datatypes.tabular:Sam
galaxy.datatypes.registry DEBUG 2011-10-21 00:28:30,670 Loaded sniffer for datatype: galaxy.datatypes.images:Jpg
galaxy.datatypes.registry DEBUG 2011-10-21 00:28:30,671 Loaded sniffer for datatype: galaxy.datatypes.images:Png
galaxy.datatypes.registry DEBUG 2011-10-21 00:28:30,671 Loaded sniffer for datatype: galaxy.datatypes.images:Tiff
galaxy.datatypes.registry DEBUG 2011-10-21 00:28:30,671 Loaded sniffer for datatype: galaxy.datatypes.images:Bmp
galaxy.datatypes.registry DEBUG 2011-10-21 00:28:30,671 Loaded sniffer for datatype: galaxy.datatypes.images:Gif
galaxy.datatypes.registry DEBUG 2011-10-21 00:28:30,671 Loaded sniffer for datatype: galaxy.datatypes.images:Im
galaxy.datatypes.registry DEBUG 2011-10-21 00:28:30,671 Loaded sniffer for datatype: galaxy.datatypes.images:Pcd
galaxy.datatypes.registry DEBUG 2011-10-21 00:28:30,671 Loaded sniffer for datatype: galaxy.datatypes.images:Pcx
galaxy.datatypes.registry DEBUG 2011-10-21 00:28:30,671 Loaded sniffer for datatype: galaxy.datatypes.images:Ppm
galaxy.datatypes.registry DEBUG 2011-10-21 00:28:30,671 Loaded sniffer for datatype: galaxy.datatypes.images:Psd
galaxy.datatypes.registry DEBUG 2011-10-21 00:28:30,671 Loaded sniffer for datatype: galaxy.datatypes.images:Xbm
galaxy.datatypes.registry DEBUG 2011-10-21 00:28:30,671 Loaded sniffer for datatype: galaxy.datatypes.images:Xpm
galaxy.datatypes.registry DEBUG 2011-10-21 00:28:30,671 Loaded sniffer for datatype: galaxy.datatypes.images:Rgb
galaxy.datatypes.registry DEBUG 2011-10-21 00:28:30,671 Loaded sniffer for datatype: galaxy.datatypes.images:Pbm
galaxy.datatypes.registry DEBUG 2011-10-21 00:28:30,671 Loaded sniffer for datatype: galaxy.datatypes.images:Pgm
galaxy.datatypes.registry DEBUG 2011-10-21 00:28:30,671 Loaded sniffer for datatype: galaxy.datatypes.images:Xpm
galaxy.datatypes.registry DEBUG 2011-10-21 00:28:30,671 Loaded sniffer for datatype: galaxy.datatypes.images:Eps
galaxy.datatypes.registry DEBUG 2011-10-21 00:28:30,672 Loaded sniffer for datatype: galaxy.datatypes.images:Rast
galaxy.model.migrate.check DEBUG 2011-10-21 00:28:30,685 psycopg2 egg successfully loaded for postgres dialect
Traceback (most recent call last):
  File "/home/koala2/galaxy-dist/lib/galaxy/web/buildapp.py", line 82, in app_factory
    app = UniverseApplication( global_conf = global_conf, **kwargs )
  File "/home/koala2/galaxy-dist/lib/galaxy/app.py", line 33, in __init__
    create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options )
  File "/home/koala2/galaxy-dist/lib/galaxy/model/migrate/check.py", line 54, in create_or_verify_database
    dataset_table = Table( "dataset", meta, autoload=True )
  File "/home/koala2/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/schema.py", line 108, in __call__
    return type.__call__(self, name, metadata, *args, **kwargs)
  File "/home/koala2/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/schema.py", line 236, in __init__
    _bind_or_error(metadata).reflecttable(self, include_columns=include_columns)
  File "/home/koala2/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py", line 1261, in reflecttable
    conn = self.contextual_connect()
  File "/home/koala2/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py", line 1229, in contextual_connect
    return self.Connection(self, self.pool.connect(), close_with_result=close_with_result, **kwargs)
  File "/home/koala2/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/pool.py", line 142, in connect
    return _ConnectionFairy(self).checkout()
  File "/home/koala2/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/pool.py", line 304, in __init__
    rec = self._connection_record = pool.get()
  File "/home/koala2/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/pool.py", line 161, in get
    return self.do_get()
  File "/home/koala2/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/pool.py", line 639, in do_get
    con = self.create_connection()
  File "/home/koala2/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/pool.py", line 122, in create_connection
    return _ConnectionRecord(self)
  File "/home/koala2/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/pool.py", line 198, in __init__
    self.connection = self.__connect()
  File "/home/koala2/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/pool.py", line 261, in __connect
    connection = self.__pool._creator()
  File "/home/koala2/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.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

Turns out that my server is not starting too:

koala2@aedes:~$ sudo /etc/init.d/proftpd start
 * Starting ftp server proftpd 
- Fatal: unknown configuration directive 'SQLPasswordEngine' on line 43 of '/etc/proftpd/proftpd.conf'     [fail]

I checked the the proftpd.conf that I prepared:

42 # Set up mod_sql_password - Galaxy passwords are stored as hex-encoded SHA1
43 SQLPasswordEngine                 on
44 SQLPasswordEncoding             hex

Any suggestion how to solve it. I was using the my local instance before, but getting the files from Amazon s3 buckets, but that takes too long and I am not using the cloud anymore.
Thank you.

Luciano















On Thu, Oct 20, 2011 at 6:59 PM, Greg Von Kuster <greg@bx.psu.edu> wrote:
Luciano,

You only need to create the database instance itself, you do not need to manually create any tables.  When you have created the database instance, configure the path to it using the database_connection setting in universe_wsgi.ini, something like:


This is all you need to do.  Then start up the Galaxy server with:

sh run.sh

and Galaxy will automatically create all of the necessary tables for you.

Greg Von Kuster

On Oct 20, 2011, at 7:44 PM, Luciano Cosme wrote:

Hi,
   I am sorry about the trivial questions. I am following this guide http://wiki.g2.bx.psu.edu/Admin/Config/Upload%20via%20FTP to set up a ftp server to upload data to my local instance of galaxy. I am getting a error when I am configuring the database server:

postgres@aedes:~$ createuser -SDR galaxyftp
postgres@aedes:~$ psql galaxydb
psql (9.1.1)
Type "help" for help.

galaxydb=# ALTER ROLE galaxyftp PASSWORD 'dbpassword';
ALTER ROLE
galaxydb=# GRANT SELECT ON galaxy_user TO galaxyftp;
ERROR:  relation "galaxy_user" does not exist
galaxydb=#


It might be something pretty simple, but I am new to it and any help will be appreciated. I create the user galaxy_user already.

Thank you.
Luciano
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Greg Von Kuster
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Greg Von Kuster
Galaxy Development Team
greg@bx.psu.edu