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 <g...@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:
>
> database_connection =
> postgres:///galaxy_dbt?user=postgres&password=postgres
>
> 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
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
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>
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>
>
> Greg Von Kuster
> Galaxy Development Team
> g...@bx.psu.edu
>
>
>
>
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