Very slow start up of local Galaxy instance

Question: Very slow start up of local Galaxy instance

8 months ago by

Germany

e.rempel • 30 wrote:

Hi all,

yesterday I have encountered a problem of a very slow (several minutes) start-up of a local Galaxy instance. Using

tail -f paster.log

I saw some kind of a loop: lines were reappearing over and over again. The output of

tail -f paster.log | grep 'Adding an entry for version 0.7.1 of package bx-python'

tool_shed.galaxy_install.installed_repository_manager DEBUG 2018-03-22 19:37:50,918 Adding an entry for version 0.7.1 of package bx-python to installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies. tool_shed.galaxy_install.installed_repository_manager DEBUG 2018-03-22 19:37:51,425 Adding an entry for version 0.7.1 of package bx-python to runtime_tool_dependencies_of_installed_tool_dependencies. tool_shed.galaxy_install.installed_repository_manager DEBUG 2018-03-22 19:37:58,268 Adding an entry for version 0.7.1 of package bx-python to installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies. tool_shed.galaxy_install.installed_repository_manager DEBUG 2018-03-22 19:38:12,457 Adding an entry for version 0.7.1 of package bx-python to runtime_tool_dependencies_of_installed_tool_dependencies. tool_shed.galaxy_install.installed_repository_manager DEBUG 2018-03-22 19:38:22,195 Adding an entry for version 0.7.1 of package bx-python to installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies. tool_shed.galaxy_install.installed_repository_manager DEBUG 2018-03-22 19:38:22,281 Adding an entry for version 0.7.1 of package bx-python to runtime_tool_dependencies_of_installed_tool_dependencies. tool_shed.galaxy_install.installed_repository_manager DEBUG 2018-03-22 19:38:28,005 Adding an entry for version 0.7.1 of package bx-python to installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies. tool_shed.galaxy_install.installed_repository_manager DEBUG 2018-03-22 19:39:50,186 Adding an entry for version 0.7.1 of package bx-python to runtime_tool_dependencies_of_installed_tool_dependencies. tool_shed.galaxy_install.installed_repository_manager DEBUG 2018-03-22 19:39:56,245 Adding an entry for version 0.7.1 of package bx-python to installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies. tool_shed.galaxy_install.installed_repository_manager DEBUG 2018-03-22 19:40:44,421 Adding an entry for version 0.7.1 of package bx-python to runtime_tool_dependencies_of_installed_tool_dependencies. tool_shed.galaxy_install.installed_repository_manager DEBUG 2018-03-22 19:40:50,370 Adding an entry for version 0.7.1 of package bx-python to installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies. tool_shed.galaxy_install.installed_repository_manager DEBUG 2018-03-22 19:42:09,590 Adding an entry for version 0.7.1 of package bx-python to runtime_tool_dependencies_of_installed_tool_dependencies. tool_shed.galaxy_install.installed_repository_manager DEBUG 2018-03-22 19:42:09,590 Adding an entry for version 0.7.1 of package bx-python to installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies.

For me it looks like indexing of existing tool dependencies. Could it slow the start-up that much?

Thanks in advance, Eugen

software error galaxy • 342 views

ADD COMMENT • link •

modified 8 months ago by Jennifer Hillman Jackson ♦ 25k • written 8 months ago by e.rempel • 30

8 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Was your source from the latest git version of the Galaxy 18.01 release? If not, try that, or upgrade your existing instance.

A few patches have been made since the initial release, so if you happened to get it early, checking and updating to any fixes might help. This issue looks familiar. I'll ask our development team to confirm and do some testing with a fresh 18.01 checkout.

If you are working with Cloudman, that has not been upgraded yet (but will be soon). Docker Galaxy is current. https://galaxyproject.github.io/

The release notes contain all the recent changes/bug fixes made at the time of the release: https://docs.galaxyproject.org/en/master/releases/18.01_announce.html

Changes made since the initial release can be tracked at the Galaxy repository: https://github.com/galaxyproject/galaxy/tree/release_18.01

Please let us know if the update resolves the issue. If not, we can look into this more.

Thanks, Jen, Galaxy team

ADD COMMENT • link written 8 months ago by Jennifer Hillman Jackson ♦ 25k

Hi Jen,

thank you for your response. Actually, we are still using the 17.01 version. We are going to update it in next months. Hopefully, this issue would go away. In the meantime, if there is something we can try to remedy, please, let me know.

Best, Eugen

ADD REPLY • link written 8 months ago by e.rempel • 30

This tool's repository and dependencies have changed since 17.01. Upgrading Galaxy will definitely resolve the problem. This tool and the associated tools are linked to the primary code base.

If installing the newest version of tools, and not just this tool, but most recent upgrades, can be problematic in older Galaxy versions.

The best solution is to update your instance, as you have planned.

Another (probably, you'll need to test) is to install an earlier version of the tool, one dated in the ToolShed around the same frame. In short, use tool versions that were developed to work with the Galaxy server version in use.

ADD REPLY • link modified 8 months ago • written 8 months ago by Jennifer Hillman Jackson ♦ 25k

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