Many errors on install : Zlib, Samtools, cutadapt, galaxy utils

Question: Many errors on install : Zlib, Samtools, cutadapt, galaxy utils

3.0 years ago by

France

Hello everyone,

I have many errors when I try to install some tools from the toolshed. Some of them were properly installed on an older instance. So I think the network may have changed some security rules. But I am not sure actually, and I have no idea about the way to proceed to find the origin of this problem.

I will list here the errors that I observe. Maybe you will have a clue about what is wrong with this local instance. My guess is that it is related to the network, but it could be that I lack some new libraries... I don't know.

package_zlib_1_2_8 , package_samtools_1_1 , cutadapt 1.6

Error The installation directory for this tool dependency had contents but the database had no record. The installation log may show this tool dependency to be correctly installed, but due to the missing database record it is now being set to Error.

and another error galaxy utils 1.0.0 : A: Package Galaxy Utils error on installation

I hope that this errors are known, this is really troublesome for my work.

Thank you!

Christ

installation network error • 1.1k views

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modified 3.0 years ago • written 3.0 years ago by christophe.habib • 340

3.0 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello, Are you running the the current Master branch of Galaxy? Was tool_dependency_dir defined in config/galaxy.ini then the server restarted? Thanks, Jen, Galaxy team

ADD COMMENT • link written 3.0 years ago by Jennifer Hillman Jackson ♦ 25k

Hello! Yes I am running the current master branch for galaxy, and I defined a tool_dependency_dir in my galaxy.ini. Thanks, Christ

ADD REPLY • link written 3.0 years ago by christophe.habib • 340

Some changes were just implemented today a bit ago for at least one of these packages (Galaxy Utils). Could you try it now? Uninstall the originals (fully) then update: C: Package Galaxy Utils error on installation

ADD REPLY • link written 3.0 years ago by Jennifer Hillman Jackson ♦ 25k

Hi Jen, I installed properly the galaxy utils package. But there is no change for the 3 others. Thanks for your help

ADD REPLY • link written 3.0 years ago by christophe.habib • 340

Our team is looking into the issues with the other packages. Please follow this Github ticket for progress: https://github.com/galaxyproject/tools-devteam/issues/283

Thanks again for reporting the problem! Jen

ADD REPLY • link written 3.0 years ago by Jennifer Hillman Jackson ♦ 25k

3.0 years ago by

christophe.habib • 340

France

christophe.habib • 340 wrote:

Hello. Did you do something to correct this ? It seems that the 3 packages work fine now.

ADD COMMENT • link written 3.0 years ago by christophe.habib • 340

Our team is confirming this, but glad that it is working for you! Jen

ADD REPLY • link written 3.0 years ago by Jennifer Hillman Jackson ♦ 25k

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