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
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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/
