I'm using galxy-dist. That's why I don't have the setting. Thanks for
the information, I'll wait for the next stable release and update the
settings then.
Geert
On 03/26/2014 01:59 PM, Greg Von Kuster wrote:
The changeset that made this a configurable setting was committed to
the stable branch ind270d3c, which was committed on 2014-02-19
https://bitbucket.org/galaxy/galaxy-central/commits/d270d3cf7627a42b6fac2aa69701deadb89c8ffc
If you are tracking the stable branch in the galaxy central repo
(which it looks like you are doing), then you should be able to pull
it from there.
Greg Von Kuster
On Mar 26, 2014, at 8:04 AM, Geert Vandeweyer
<[email protected]
<mailto:[email protected]>> wrote:
Hi Greg,
The setting was not in my universe_sample file. I added it, set
log_info to DEBUG and restarted galaxy.
The startup time remained the same, and there were many entries in
the log file indicating that the lag is indeed the creation of the
dependency system:
tool_shed.galaxy_install.installed_repository_manager DEBUG
2014-03-26 13:01:01,176 Adding an entry for version 0.1.18 of package
samtools to runtime_tool_dependencies_of_installed_tool_dependencies.
tool_shed.galaxy_install.installed_repository_manager DEBUG
2014-03-26 13:01:02,645 Adding an entry for version 0.1.18 of package
samtools to
installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies.
tool_shed.galaxy_install.installed_repository_manager DEBUG
2014-03-26 13:01:03,874 Adding an entry for version 0.1.18 of package
samtools to runtime_tool_dependencies_of_installed_tool_dependencies.
tool_shed.galaxy_install.installed_repository_manager DEBUG
2014-03-26 13:01:05,383 Adding an entry for version 0.1.18 of package
samtools to
installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies.
tool_shed.galaxy_install.installed_repository_manager DEBUG
2014-03-26 13:01:06,533 Adding an entry for version 2.11.0 of package
R to runtime_tool_dependencies_of_installed_tool_dependencies.
tool_shed.galaxy_install.installed_repository_manager DEBUG
2014-03-26 13:01:08,054 Adding an entry for version 2.11.0 of package
R to
installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies.
tool_shed.galaxy_install.installed_repository_manager DEBUG
2014-03-26 13:01:09,126 Adding an entry for version 2.11.0 of package
R to runtime_tool_dependencies_of_installed_tool_dependencies.
tool_shed.galaxy_install.installed_repository_manager DEBUG
2014-03-26 13:01:10,596 Adding an entry for version 2.11.0 of package
R to
installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies.
tool_shed.galaxy_install.installed_repository_manager DEBUG
2014-03-26 13:01:11,803 Adding an entry for version 1.02.00 of
package lastz to
runtime_tool_dependencies_of_installed_tool_dependencies.
tool_shed.galaxy_install.installed_repository_manager DEBUG
2014-03-26 13:01:13,332 Adding an entry for version 1.02.00 of
package lastz to
installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies.
tool_shed.galaxy_install.installed_repository_manager DEBUG
2014-03-26 13:01:14,552 Adding an entry for version 3.0.1 of package
R_3_0_1 to runtime_tool_dependencies_of_installed_tool_dependencies.
tool_shed.galaxy_install.installed_repository_manager DEBUG
2014-03-26 13:01:15,943 Adding an entry for version 3.0.1 of package
R_3_0_1 to
installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies.
tool_shed.galaxy_install.installed_repository_manager DEBUG
2014-03-26 13:01:17,162 Adding an entry for version 0.1.18 of package
samtools to runtime_tool_dependencies_of_installed_tool_dependencies.
tool_shed.galaxy_install.installed_repository_manager DEBUG
2014-03-26 13:01:18,594 Adding an entry for version 0.1.18 of package
samtools to
installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies.
etc...
I also note many double entries in the log files.
Do I need a specific changeset for the parameter setting to take effect?
Universe_wsgi.ini setting:
# Enable use of an in-memory registry with bi-directional
relationships between repositories
manage_dependency_relationships = False
Best,
Geert
On 03/26/2014 11:53 AM, Greg Von Kuster wrote:
Hi Geert,
The setting should be in your universe_wsgi.ini.sample, and you woud
have to manually edit your universe_wsgi.ini to add it. I would say
that 125 installed packages is probably what is causing the slow
starts. This feature is not currently useful, so it can be set to
not function with no problems. In the future I'll introduce
additional benefits for this feature, and I'll look at ways to
improve the startup speed.
Greg Von Kuster
On Mar 26, 2014, at 3:43 AM, Geert Vandeweyer
<[email protected]
<mailto:[email protected]>> wrote:
hi Greg,
I don't have that setting in my universe. Should I just add it? The
output of hg summary is (hg incoming doesn't show any available
updates):
parent: 12276:dc067a95261d tip
Added tag release_2014.02.10 for changeset 5e605ed6069f
branch: stable
commit: 22 modified, 1 deleted, 127 unknown
update: (current)
I currently have 125 packages from toolsheds. Is that considered to
be "many"? Most of them are the migrated tools and the devteam
mappers/gatk/tophat stuff.
Geert
On 03/25/2014 05:16 PM, Greg Von Kuster wrote:
Hello Geert,
Do you have a lot of repositories installed from the Tool Shed
into you Galaxy instance? if so, the time you're experience may
be due to loading the in-memory installed repository registry.
Using this registry is optional, but the default configuration
setting is to use it. You can set the following to entry to False
in your universe_wsgi.ini file and restart your Galaxy server to
see if that is the problem. This registry is not currently used
by anythin except to display the set of dependent repositories
that will be affected if a repository is uninstalled. If this is
ot what is causing the slow statup, then I'm not sure where else
to look.
# Enable use of an in-memory registry with bi-directional
relationships
# between repositories (i.e., in addition to lists of dependencies
for a
# repository, keep an in-memory registry of dependent items for
each repository.
#manage_dependency_relationships = True
Greg Von Kuster
On Mar 25, 2014, at 11:08 AM, Geert Vandeweyer
<[email protected]
<mailto:[email protected]>> wrote:
Dear all,
I'm wondering if the following behaviour is normal. Since I
reinstalled the latest galaxy distribution, every restart
hangs/loads for up to 10 minutes at the following lines:
galaxy.model.migrate.check INFO 2014-03-25 15:56:57,965 At
database version 118
tool_shed.galaxy_install.migrate.check INFO 2014-03-25
15:56:58,477 At migrate_tools version 9
galaxy.config INFO 2014-03-25 15:56:58,694 Install database
targetting Galaxy's database configuration.
After several minutes of no heavy processing (cpu/database is
almost idle), the startup continues.
Best,
Geert
--
Geert Vandeweyer, Ph.D.
Department of Medical Genetics
University of Antwerp
Prins Boudewijnlaan 43
2650 Edegem
Belgium
Tel: +32 (0)3 275 97 56
E-mail: [email protected] <mailto:[email protected]>
http://ua.ac.be/cognitivegenetics
http://www.linkedin.com/in/geertvandeweyer
___________________________________________________________
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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--
Geert Vandeweyer, Ph.D.
Department of Medical Genetics
University of Antwerp
Prins Boudewijnlaan 43
2650 Edegem
Belgium
Tel: +32 (0)3 275 97 56
E-mail:[email protected]
http://ua.ac.be/cognitivegenetics
http://www.linkedin.com/in/geertvandeweyer
--
Geert Vandeweyer, Ph.D.
Department of Medical Genetics
University of Antwerp
Prins Boudewijnlaan 43
2650 Edegem
Belgium
Tel: +32 (0)3 275 97 56
E-mail:[email protected]
http://ua.ac.be/cognitivegenetics
http://www.linkedin.com/in/geertvandeweyer
___________________________________________________________
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/
--
Geert Vandeweyer, Ph.D.
Department of Medical Genetics
University of Antwerp
Prins Boudewijnlaan 43
2650 Edegem
Belgium
Tel: +32 (0)3 275 97 56
E-mail: [email protected]
http://ua.ac.be/cognitivegenetics
http://www.linkedin.com/in/geertvandeweyer
___________________________________________________________
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/
