Fatal error: Exit code 127 () and conda issue

Question: Fatal error: Exit code 127 () and conda issue

16 months ago by

n.goue • 50

n.goue • 50 wrote:

Hi, I am trying and use VCF-BEDintersect tool that I have installed through the toolshed. Installation was successful, but when I try using it, it ends up with this error:

Fatal error: Exit code 127 () xxx/galaxy/database/jobs_directory/000/73/tool_script.sh: ligne 9: vcfintersect : command not found.

From other posts, it is mentioned that Conda could be involved in that, and actually from the log file, I noticed another error:

/bin/sh: 1: /xxx/galaxy/database/dependencies/_conda/bin/conda: not found

However, Conda exe is present in that folder and galaxy can have access it. So what's wrong ?

I am using latest Galaxy, and I have updated the dependency_resolvers_conf.xml with Conda as first choice.

Any ideas?

Thanks,

galaxy • 840 views

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modified 16 months ago • written 16 months ago by n.goue • 50

16 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The tool is actually vcfbedintersect correct? The error mentions vcfintersect which is a dependency for this tool and also for vcfvcfintersect and some others from this tool group.

The tool vcfbedintersect has a revision date from 2016 and has not been converted to conda-dependency management. Instead, these use the original dependency packages from the Tool Shed.

From the tool's macros.xmll:

<xml name="requirements">
    <requirements>
        <requirement type="package" version="1.0.0_rc1">vcflib</requirement>
        <yield/>
    </requirements>
</xml>

This is the specific package that should have been installed with the tool: suite_vcflib_1_0_0_rc1

Perhaps try installing that directly to see if the tool problems resolve?

Thanks, Jen, Galaxy team

ADD COMMENT • link written 16 months ago by Jennifer Hillman Jackson ♦ 25k

16 months ago by

n.goue • 50

n.goue • 50 wrote:

Hi Jen,

I installed the tool suite_vcfkib_1_0_0_rc1 and it solved the problem. The tool is now working nicely. Also, no more conda error .

Thank you for your kind help !

ADD COMMENT • link written 16 months ago by n.goue • 50

Great, I'm glad that worked but still concerned that packages seem to not be installed by default (as they should for tools that do not use Conda (yet - or in some case maybe never). So you know, this has come up for others and I've asked the development team about it. Does not seem to be restricted to Docker galaxy but that is not confirmed yet.

Meanwhile, the workaround is to install missing packages directly, as you have done.

ADD REPLY • link written 16 months ago by Jennifer Hillman Jackson ♦ 25k

16 months ago by

n.goue • 50

n.goue • 50 wrote:

Thank you Jen, for the explanation.

ADD COMMENT • link written 16 months ago by n.goue • 50

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