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
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
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: geert.vandeweyer@ua.ac.be
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: geert.vandeweyer@ua.ac.be
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: geert.vandeweyer@ua.ac.be
http://ua.ac.be/cognitivegenetics
http://www.linkedin.com/in/geertvandeweyer