Re: [galaxy-dev] Cluster jobs running as real user
Follow the Galaxy wiki https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#Submitting_Jobs_as_the_Real_User setup permission instructions. Follow these 2 steps to get Galaxy to run as real users with IBM Platform LSF: Step 1) Download the latest LSF DRMAA 1.1.1 from github. https://github.com/PlatformLSF/lsf-drmaa Level commit e4d5c1ab10fcba572eaede68fc2fc05332198bec or above This fixes the LSF job id not found issue. Step 2) LSF needs to disable message being printed out via the LSF environment variable BSUB_QUIET. This can be done either in in Galaxy drmaa_external_runner.py file or in the galaxy admin environment profile Edit the drmaa_external_runner.py file to add in the LSF environment variable BSUB_QUIET to disable message print out. Line in blue below. scripts/drmaa_external_runner.py: def main(): userid, json_filename, assign_all_groups = validate_paramters() set_user(userid, assign_all_groups) json_file_exists(json_filename) os.environ['BSUB_QUIET'] = 'Y' s = drmaa.Session() s.initialize() jt = s.createJobTemplate() load_job_template_from_file(jt, json_filename) OR Disable LSF message in the galaxy admin profile e.g. export BSUB_QUIET=Y in .bash_profile Regards, Linda___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] toolshed repository down?
Hi.
Getting error when trying to install the latest Galaxy on a new stand alone
linux RH server. Is the repository down?
migrate.versioning.repository DEBUG 2013-07-16 14:14:46,235 Config:
{'db_settings': {'__name__': 'db_settings', 'required_dbs': '[]',
'version_table': 'migrate_tools', 'repository_id': '
GalaxyTools'}}
tool_shed.galaxy_install.migrate.check DEBUG 2013-07-16 14:14:46,240
psycopg2 egg successfully loaded for postgres dialect
The URL
http://toolshed.g2.bx.psu.edu/repository/get_tool_dependencies?name=bowtie_wrappersowner=devteamchangeset_revision=0c7e4eadfb3cfrom_install_manager=True
raised the exception:
urlopen error [Errno 110] Connection timed out
The URL
http://toolshed.g2.bx.psu.edu/repository/get_tool_dependencies?name=bowtie_color_wrappersowner=devteamchangeset_revision=fd0914e451c5from_install_manager=True
raised the exception:
urlopen error [Errno 110] Connection timed out
The URL
http://toolshed.g2.bx.psu.edu/repository/get_tool_dependencies?name=lastzowner=devteamchangeset_revision=0801f8207d30from_install_manager=True
raised the exception:
urlopen error [Errno 110] Connection timed out
The URL
http://toolshed.g2.bx.psu.edu/repository/get_tool_dependencies?name=lastz_paired_readsowner=devteamchangeset_revision=96825cee5c25from_install_manager=True
raised the exception:
urlopen error [Errno 110] Connection timed out
Traceback (most recent call last):
...
return tool_shed_accessible, missing_tool_configs_dict
UnboundLocalError: local variable 'missing_tool_configs_dict' referenced
before assignment
Regards,
Linda___
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[galaxy-dev] Galaxy job will stay in waiting under DRMAA runner until manually trigger a command line submission
Hi. Running standalone Galaxy stable_2013.06.03 version on RH6.2 with postgresl db with GPFS filesystem. Setup via the directions in http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster to run all jobs through the LSF DRMAA runner. job_conf.xml: job_conf plugins plugin id=drmaa type=runner load=galaxy.jobs.runners.drmaa:DRMAAJobRunner workers=4/ /plugins handlers handler id=main/ /handlers destinations default=lsf destination id=lsf runner=drmaa/ /destinations /job_conf Scheduler and Galaxy were started. Submit a FASTQ groomer job on a FASTQ file under Galaxy. The groomer job in History will stay in GREY Job is waiting to run state until one physically go onto the node and submits a command line job through the scheduler. Once that command line job (e.g. sleep 5) is submitted then the groomer job will show up in the scheduler's job queue and galaxy's HISTORY will now show it as running. I can submit another groomer job after this and it will show up as running. At times, one will see this type of scenario again where one has to manually start a job under the scheduler on the command line to trigger the galaxy's jobs to start running under the scheduler. Is there some setup I am missing in the job_conf.xml above or a flag not set in universe_wsgi.ini? Searching the Galaxy web, I had read that one can set the track_jobs_in_database=True to trigger it to look in memory or database. But that didn't work either. Wonder if anyone seen this type of issue with any runners and have any suggestions on how to debug and fix this. Thanks. Linda___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Installation of 20130603 Galaxy image with MySQL fails
Thanks Dannon. I am going with postgres for now while mysql is being fixed. Regards, Linda From: Dannon Baker dannon.ba...@gmail.com To: Linda Cham/Poughkeepsie/IBM@IBMUS Cc: Björn Grüning bjoern.gruen...@pharmazie.uni-freiburg.de, Galaxy Dev galaxy-dev@lists.bx.psu.edu Date: 06/06/2013 04:41 PM Subject:Re: [galaxy-dev] Installation of 20130603 Galaxy image with MySQL fails Hi Linda, Sorry I wasn't clear before. The fix for that first issue is in galaxy-central's stable branch, which will be migrated to galaxy-dist probably sometime next week. You can always pull directly from -central though, using 'hg pull -u -b stable http://bitbucket.org/galaxy/galaxy-central/' That said, this doesn't resolve the mysql index issues, which I'm currently working on. I hope to have a fix for them available soon, though. -Dannon On Wed, Jun 5, 2013 at 4:47 PM, Linda Cham lc...@us.ibm.com wrote: Hi Bjorn, Currently seen $ hg tip changeset: 9850:cea3ddf6cdda branch: stable tag: tip user: Nate Coraor n...@bx.psu.edu date: Mon Jun 03 16:17:31 2013 -0400 summary: Update tag for stable_2013.06.03 Removed galaxy-dist directory and rerun the hg clone command. $ hg clone https://bitbucket.org/galaxy/galaxy-dist#stable destination directory: galaxy-dist requesting all changes adding changesets adding manifests adding file changes added 9851 changesets with 36400 changes to 7175 files updating to branch stable 4132 files updated, 0 files merged, 0 files removed, 0 files unresolved $ cd galaxy-dist $ hg heads changeset: 9850:cea3ddf6cdda branch: stable tag: tip user: Nate Coraor n...@bx.psu.edu date: Mon Jun 03 16:17:31 2013 -0400 summary: Update tag for stable_2013.06.03 $ hg pull ; hg update stable pulling from https://bitbucket.org/galaxy/galaxy-dist searching for changes no changes found 0 files updated, 0 files merged, 0 files removed, 0 files unresolved Check the script/manage_db.py: from galaxy import eggs - No decorator line eggs.require( Tempita ) eggs.require( SQLAlchemy ) eggs.require( sqlalchemy_migrate ) $ hg update tip 0 files updated, 0 files merged, 0 files removed, 0 files unresolved $ hg heads changeset: 9850:cea3ddf6cdda branch: stable tag: tip user: Nate Coraor n...@bx.psu.edu date: Mon Jun 03 16:17:31 2013 -0400 summary: Update tag for stable_2013.06.03 $ hg update default 82 files updated, 0 files merged, 2 files removed, 0 files unresolved $ hg heads changeset: 9850:cea3ddf6cdda branch: stable tag: tip user: Nate Coraor n...@bx.psu.edu date: Mon Jun 03 16:17:31 2013 -0400 summary: Update tag for stable_2013.06.03 script/manage_db.py still the same as above. Inactive hide details for Björn Grüning ---06/05/2013 04:30:09 PM---Hi Linda, Hi Dannon,Björn Grüning ---06/05/2013 04:30:09 PM---Hi Linda, Hi Dannon, From: Björn Grüning bjoern.gruen...@pharmazie.uni-freiburg.de To: Linda Cham/Poughkeepsie/IBM@IBMUS Cc: Dannon Baker dannon.ba...@gmail.com, Galaxy Dev galaxy-dev@lists.bx.psu.edu Date: 06/05/2013 04:30 PM Subject: Re: [galaxy-dev] Installation of 20130603 Galaxy image with MySQL fails Hi Linda, Hi Dannon, Thanks. I tried to do the hg pull and update and hg tip but I do not see the changes in my working directory. So I added the one liner eggs.require( decorator ) to scripts/manage_db.py. Ran the sh manage_db.sh upgrade and get this error: that is really strange. Can you show us what the output of hg tip is? Do you mind to start with a fresh checkout and that particular change? Thanks, Björn inline: graycol.gif___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Trackster set display mode - Output looks all the same
Thank you Jeremy. The new wiki page looks great! Regards, Linda From: Jeremy Goecks jeremy.goe...@emory.edu To: Linda Cham/Poughkeepsie/IBM@IBMUS Cc: galaxy-dev@lists.bx.psu.edu Date: 06/11/2013 12:56 PM Subject:Re: [galaxy-dev] Trackster set display mode - Output looks all the same Hi Linda, 1- Should the Set display mode give out different output? Not yet. VCF visualization is new to Galaxy, and mode switching isn't implemented yet. (It will be implemented in the next release.) What you're seeing is the display of individual variants; of course, trying to view so many variants leads to the mismash that you noted. If you zoom in sufficiently, you should see variants without trouble. See the attached screenshot for example. 2- What might be the issue if all I see are the same output or maybe the output displayed is totally incorrect? Might there be some trackster setup that I might be missing for it to draw incorrectly? Everything looks OK so far. FYI, I've created a new page that lists the steps for setting up visualization for a Galaxy instance and updated wiki links/text to point to this page: http://wiki.galaxyproject.org/Visualization%20Setup Best, J.inline: graycol.gifinline: 1C299461.gif___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] GATK
Hi Sridhar, About the error, you need to request a key from GATK http://gatkforums.broadinstitute.org/discussion/1250/what-is-phone-home-and-how-does-it-affect-me#latest See under How to obtain and use a GATK key Or by pass it by removing the -et NO_ET line from the xml files. From: sridhar srinivasan sridhar2bioi...@gmail.com To: Galaxy Dev galaxy-dev@lists.bx.psu.edu Date: 06/06/2013 06:30 AM Subject:[galaxy-dev] GATK Sent by:galaxy-dev-boun...@lists.bx.psu.edu Dear Developers, I am running GATK for first time. In galaxy i use Unified Genotyper. I am getting error as below mentioned. # ERROR -- # ERROR A USER ERROR has occurred (version 2.5-2-gf57256b): # ERROR The invalid arguments or inputs must be corrected before the GATK can proceed # ERROR Please do not post this error to the GATK forum # ERROR # ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments. # ERROR Visit our website and forum for extensive documentation and answers to # ERROR commonly asked questions http://www.broadinstitute.org/gatk # ERROR # ERROR MESSAGE: Running with the -et NO_ET or -et STDOUT option requires a GATK Key file. Please see http://gatkforums.broadinstitute.org/discussion/1250/what-is-phone-home-and-how-does-it-affect-me#latest for more information and instructions on how to obtain a key. # ERROR -- also suggest me about the Rod file for dbSNP. Thanks Sridhar___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/inline: graycol.gif___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Installation of 20130603 Galaxy image with MySQL fails
Hi. I am new to the Galaxy forum and I am trying to setup a new local
Galaxy instance with MySQL on RH6.2 x86_64.
On a newly installed OS node, using the hg clone command (hg clone
https://bitbucket.org/galaxy/galaxy-dist#stable) which gets the current
Galaxy 20130603 image, I am getting the following errors when running
run.sh:
File build/bdist.linux-x86_64-ucs4/egg/MySQLdb/cursors.py, line 173, in
execute
self.errorhandler(self, exc, value)
File build/bdist.linux-x86_64-ucs4/egg/MySQLdb/connections.py, line 36,
in defaulterrorhandler
raise errorclass, errorvalue
OperationalError: (OperationalError) (1170, BLOB/TEXT column 'slug' used
in key specification without a key length) 'CREATE INDEX ix_history_slug
ON history (slug)' ()
Reading the forum, someone stated it can be bypass by running the CREATE
INDEX.
mysql CREATE INDEX ix_history_slug ON history (slug(1000));
Query OK, 0 rows affected (0.09 sec)
Records: 0 Duplicates: 0 Warnings: 0
When trying to run.sh again after the CREATE INDEX, will get this error:
File /gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/lib/galaxy/app.py, line
52, in __init__
create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get
( '__file__', None ), self.config.database_engine_options, app=self )
File
/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/lib/galaxy/model/migrate/check.py,
line 107, in create_or_verify_database
% ( db_schema.version, migrate_repository.versions.latest,
config_arg ) )
Exception: Your database has version '29' but this code expects version
'115'. Please backup your database and then migrate the schema by running
'sh manage_db.sh upgrade'.
So try to run the sh manage_db.sh upgrade' now will get this error:
$ sh manage_db.sh upgrade
Traceback (most recent call last):
File ./scripts/manage_db.py, line 13, in module
from migrate.versioning.shell import main
File
/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/shell.py,
line 12, in module
from migrate.versioning import api
File
/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/api.py,
line 33, in module
from migrate.versioning import (repository, schema, version,
File
/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/repository.py,
line 13, in module
from migrate.versioning import version, pathed, cfgparse
File
/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/version.py,
line 10, in module
from migrate.versioning import pathed, script
File
/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/pathed.py,
line 11, in module
from migrate.versioning.util import KeyedInstance
File
/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/util/__init__.py,
line 7, in module
from decorator import decorator
ImportError: No module named decorator
In some searches, there were tips of deleting the eggs directory and rerun
run.sh or use a python env. Neither option worked.
Was not able to find anything meaningful about the decorator error.
Note:, I was able to get Galaxy up with MySQL using the Galaxy 788cd3d06541
image on a different node. So I am thinking maybe it is the new 20130603
image that is giving me issues?
Commands used to get Galaxy up:
Install mysql from yum repository [MySQL 5.1.52-1.el6_0.1]
python version [2.6.6]
Grant ALL PRIVILEGES galaxy_db.* TO galaxy_user on localhostname with
PWD
Images tested:
*Copy of the galaxy-galaxy-dist-788cd3d06541.tar.bz2 image Did not
run the hg update command. [This worked]
*hg clone stable of newest image [Failed]
Update the universe_wsg.ini with the port, host, database_connection to
mysql
Ran run.sh
Thanks.
Linda___
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Re: [galaxy-dev] Installation of 20130603 Galaxy image with MySQL fails
Hi Dannon,
Thanks. I tried to do the hg pull and update and hg tip but I do not see
the changes in my working directory. So I added the one liner eggs.require
( decorator ) to scripts/manage_db.py.
Ran the sh manage_db.sh upgrade and get this error:
File build/bdist.linux-x86_64-ucs4/egg/MySQLdb/cursors.py, line 173, in
execute
File build/bdist.linux-x86_64-ucs4/egg/MySQLdb/connections.py, line 36,
in defaulterrorhandler
sqlalchemy.exc.OperationalError: (OperationalError) (1060, Duplicate
column name 'slug') '\nALTER TABLE history ADD slug TEXT' ()
So I thought maybe I should remove the column that was added before.
ALTER TABLE history DROP COLUMN slug;
Ran the sh manage_db.sh upgrade again, but now it gives back the original
error:
File build/bdist.linux-x86_64-ucs4/egg/MySQLdb/connections.py, line 36,
in defaulterrorhandler
sqlalchemy.exc.OperationalError: (OperationalError) (1170, BLOB/TEXT
column 'slug' used in key specification without a key length) 'CREATE
INDEX ix_history_slug ON history (slug)' ()
Interesting to note that if I ran the sh manage_db.sh again after the
CREATE INDEX error above, I get back this error now:
File build/bdist.linux-x86_64-ucs4/egg/MySQLdb/connections.py, line 36,
in defaulterrorhandler
sqlalchemy.exc.OperationalError: (OperationalError) (1060, Duplicate
column name 'slug') '\nALTER TABLE history ADD slug TEXT' ()
Hi Linda,
The decorator issue should be resolved in galaxy-central now. I'm setting
up a test environment to see if I can reproduce the mysql issue now, and
will let you know what I come up with.
Thanks!
-Dannon
On Wed, Jun 5, 2013 at 11:12 AM, Linda Cham lc...@us.ibm.com wrote:
Hi. I am new to the Galaxy forum and I am trying to setup a new local
Galaxy instance with MySQL on RH6.2 x86_64.
On a newly installed OS node, using the hg clone command (hg clone
https://bitbucket.org/galaxy/galaxy-dist#stable) which gets the current
Galaxy 20130603 image, I am getting the following errors when running
run.sh:
File build/bdist.linux-x86_64-ucs4/egg/MySQLdb/cursors.py, line 173,
in execute
self.errorhandler(self, exc, value)
File build/bdist.linux-x86_64-ucs4/egg/MySQLdb/connections.py, line
36, in defaulterrorhandler
raise errorclass, errorvalue
OperationalError: (OperationalError) (1170, BLOB/TEXT column 'slug' used
in key specification without a key length) 'CREATE INDEX ix_history_slug
ON history (slug)' ()
Reading the forum, someone stated it can be bypass by running the CREATE
INDEX.
mysql CREATE INDEX ix_history_slug ON history (slug(1000));
Query OK, 0 rows affected (0.09 sec)
Records: 0 Duplicates: 0 Warnings: 0
When trying to run.sh again after the CREATE INDEX, will get this error:
File /gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/lib/galaxy/app.py,
line 52, in __init__
create_or_verify_database( db_url, kwargs.get( 'global_conf',
{} ).get( '__file__', None ), self.config.database_engine_options,
app=self )
File
/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/lib/galaxy/model/migrate/check.py,
line 107, in create_or_verify_database
% ( db_schema.version, migrate_repository.versions.latest,
config_arg ) )
Exception: Your database has version '29' but this code expects version
'115'. Please backup your database and then migrate the schema by
running 'sh manage_db.sh upgrade'.
So try to run the sh manage_db.sh upgrade' now will get this error:
$ sh manage_db.sh upgrade
Traceback (most recent call last):
File ./scripts/manage_db.py, line 13, in module
from migrate.versioning.shell import main
File
/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/shell.py,
line 12, in module
from migrate.versioning import api
File
/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/api.py,
line 33, in module
from migrate.versioning import (repository, schema, version,
File
/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/repository.py,
line 13, in module
from migrate.versioning import version, pathed, cfgparse
File
/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/version.py,
line 10, in module
from migrate.versioning import pathed, script
File
/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/pathed.py,
line 11, in module
from migrate.versioning.util import KeyedInstance
File
/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/util/__init__.py,
line 7, in module
from decorator import decorator
ImportError: No module named decorator
In some searches, there were tips of deleting the eggs directory and
rerun run.sh or use a python env. Neither option
Re: [galaxy-dev] Installation of 20130603 Galaxy image with MySQL fails
Hi Bjorn, Currently seen $ hg tip changeset: 9850:cea3ddf6cdda branch: stable tag: tip user:Nate Coraor n...@bx.psu.edu date:Mon Jun 03 16:17:31 2013 -0400 summary: Update tag for stable_2013.06.03 Removed galaxy-dist directory and rerun the hg clone command. $ hg clone https://bitbucket.org/galaxy/galaxy-dist#stable destination directory: galaxy-dist requesting all changes adding changesets adding manifests adding file changes added 9851 changesets with 36400 changes to 7175 files updating to branch stable 4132 files updated, 0 files merged, 0 files removed, 0 files unresolved $ cd galaxy-dist $ hg heads changeset: 9850:cea3ddf6cdda branch: stable tag: tip user:Nate Coraor n...@bx.psu.edu date:Mon Jun 03 16:17:31 2013 -0400 summary: Update tag for stable_2013.06.03 $ hg pull ; hg update stable pulling from https://bitbucket.org/galaxy/galaxy-dist searching for changes no changes found 0 files updated, 0 files merged, 0 files removed, 0 files unresolved Check the script/manage_db.py: from galaxy import eggs - No decorator line eggs.require( Tempita ) eggs.require( SQLAlchemy ) eggs.require( sqlalchemy_migrate ) $ hg update tip 0 files updated, 0 files merged, 0 files removed, 0 files unresolved $ hg heads changeset: 9850:cea3ddf6cdda branch: stable tag: tip user:Nate Coraor n...@bx.psu.edu date:Mon Jun 03 16:17:31 2013 -0400 summary: Update tag for stable_2013.06.03 $ hg update default 82 files updated, 0 files merged, 2 files removed, 0 files unresolved $ hg heads changeset: 9850:cea3ddf6cdda branch: stable tag: tip user:Nate Coraor n...@bx.psu.edu date:Mon Jun 03 16:17:31 2013 -0400 summary: Update tag for stable_2013.06.03 script/manage_db.py still the same as above. From: Björn Grüning bjoern.gruen...@pharmazie.uni-freiburg.de To: Linda Cham/Poughkeepsie/IBM@IBMUS Cc: Dannon Baker dannon.ba...@gmail.com, Galaxy Dev galaxy-dev@lists.bx.psu.edu Date: 06/05/2013 04:30 PM Subject:Re: [galaxy-dev] Installation of 20130603 Galaxy image with MySQL fails Hi Linda, Hi Dannon, Thanks. I tried to do the hg pull and update and hg tip but I do not see the changes in my working directory. So I added the one liner eggs.require( decorator ) to scripts/manage_db.py. Ran the sh manage_db.sh upgrade and get this error: that is really strange. Can you show us what the output of hg tip is? Do you mind to start with a fresh checkout and that particular change? Thanks, Björn inline: graycol.gif___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
