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

If this is on a Debian-based Linux (including Ubuntu), you probably need
something like:

    postgres:///galaxydb?host=/var/run/postgresql

As the connection string.  See the documentation at:

    http://usegalaxy.org/production

For information about that.

> 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

ProFTPD as provided by vendor packaging systems (e.g. APT) probably
don't have mod_sql_passwd compiled in.  You'll have to fix that by
compiling your own or using apt-source and building your own .deb with
it enabled.

I compiled it with the following configure args:

    ./configure --disable-auth-file --disable-ncurses               \
        --disable-ident --disable-shadow --enable-openssl           \
        --with-modules=mod_sql:mod_sql_postgres:mod_sql_passwd

--nate

> 
> 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
> > and other Galaxy lists, please use the interface at:
> >
> >  http://lists.bx.psu.edu/
> >
> >
> > Greg Von Kuster
> > Galaxy Development Team
> > g...@bx.psu.edu
> >
> >
> >
> >

> ___________________________________________________________
> 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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> 
>   http://lists.bx.psu.edu/

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