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
___________________________________________________________