Question: Galaxy could not install any tools
0
gravatar for Tianhua.He
2.7 years ago by
Tianhua.He0
Tianhua.He0 wrote:

Hello

I installed galaxy into a local machine following the instruction at https://wiki.galaxyproject.org/Admin/GetGalaxy, but was not able to install ANY tools (after set myself as admin user).

it always return me a error message as:

"Dependency was not resolved by any resolver module."

some log details as:

galaxy.tools.deps DEBUG 2016-03-04 16:57:40,260 Find dependency pca version None galaxy.tools.deps DEBUG 2016-03-04 16:57:40,260 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.nulldependency object="" at="" 0x104f47b90=""> (isnull? True) galaxy.tools.deps DEBUG 2016-03-04 16:57:40,260 Resolver galaxy_packages returned

by the way, i removed the "#" from in front of "dependency_resolvers_config_file" in galaxy.ini, it did not help either.

The dependency resolves config file specifies an ordering and options for how

Galaxy resolves tool dependencies (requirement tags in Tool XML). The default

ordering is to the use the tool shed for tools installed that way, use local

Galaxy packages, and then use conda if available.

See https://github.com/galaxyproject/galaxy/blob/dev/doc/source/admin/dependency_resolvers.rst

for more information on these options.

dependency_resolvers_config_file = config/dependency_resolvers_conf.xml

appreciate if anybody could advise how to fix it

Thank you Tianhua

galaxy • 1.4k views
ADD COMMENTlink modified 2.7 years ago by Bjoern Gruening5.1k • written 2.7 years ago by Tianhua.He0

Have you installed any dependency from the ToolShed as admin?

ADD REPLYlink written 2.7 years ago by Bjoern Gruening5.1k

No, i was not able to install anything (as admin user), and every time it returned the same error message:"Dependency was not resolved by any resolver module."

ADD REPLYlink written 2.7 years ago by Tianhua.He0

Then you need to configure Galaxy properly. Have you changed the galaxy.ini accordingly?

ADD REPLYlink written 2.7 years ago by Bjoern Gruening5.1k

Dear Bjoern,

I have tried to configure it, though I am not sure I did it properly or not (I am completely a newbie), I have the configure file attached here, it would be great if you could have a look and advise on what I missed.

By the way, the computer I installed Galaxy in is a Mac Pro, OS X Yosemite v10.10.5, and I installed galaxy under: /Users/218496f/galaxy/

Your assistance are really appreciated.

All the best Tianhua

From: Bjoern Gruening on Galaxy Biostar <notifications@biostars.org<a rel="nofollow" href="mailto:notifications@biostars.org">notifications@biostars.org> Reply-To: "galaxystar+8cc825fd+code@biostars.io<mailto:galaxystar+8cc825fd+code@biostars.io>" <galaxystar+8cc825fd+code@biostars.io<mailto:galaxystar+8cc825fd+code@biostars.io>> Date: Sunday, 6 March 2016 1:38 am To: Tianhua He <tianhua.he@curtin.edu.au<a rel="nofollow" href="mailto:Tianhua.He@curtin.edu.au">Tianhua.He@curtin.edu.au> Subject: [galaxy-biostar] Galaxy could not install any tools

Activity on a post you are following on Galaxy Biostarhttp://biostar.usegalaxy.org

User Bjoern GrueningBjoern Gruening wrote Comment: Galaxy could not install any toolsC: Galaxy could not install any tools:

Then you need to configure Galaxy properly. Have you changed the galaxy.ini accordingly?

ADD REPLYlink written 2.7 years ago by Tianhua.He0
0
gravatar for Bjoern Gruening
2.7 years ago by
Bjoern Gruening5.1k
Germany
Bjoern Gruening5.1k wrote:

Hi,

please follow this tutorial to install tools via the Galaxy Tool Shed: https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial

If you are running Galaxy on an OS-X you also might want to look at the Galaxy Docker image, which is a preconfigured - production ready Galaxy instance. For more information please read this page here: https://github.com/bgruening/docker-galaxy-stable and try to install Kitematik under OS-X.

Ciao, Bjoern

ADD COMMENTlink written 2.7 years ago by Bjoern Gruening5.1k
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