Re: [galaxy-dev] Database configuration

[Nate Coraor]

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 D

Re: [galaxy-dev] Database configuration

[Luciano Cosme]

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.datat

Re: [galaxy-dev] Database configuration

[Greg Von Kuster]

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:

Re: [galaxy-dev] Database configuration

[Greg Von Kuster]

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



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[galaxy-dev] Database configuration

[Luciano Cosme]

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/