Database configuration
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
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:
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
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:
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:
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
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:
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:
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
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 <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:
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:
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
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participants (3)
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Greg Von Kuster -
Luciano Cosme -
Nate Coraor