Toolshed INstalled tool : Job submission Failed after upgrading galaxy local instance

Question: Toolshed INstalled tool : Job submission Failed after upgrading galaxy local instance

15 months ago by

Hi galaxy community

I have been updated my local instance of galaxy to release 17.05. Since this update some tools previously installed from toolshed are not runnable : so I check the formular, fill it and click on execute and I have a red frame which appears with this message (for example bedtools, but same problem with deeptools) : The server could not complete the request. Please contact the Galaxy Team if this error persists.

{
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.24.0",
"tool_version": "2.24.0",
"inputs": {
    "inputA": {
        "values": [
            {
                "hid": 72,
                "id": "be2dfb734c2d1ff7",
                "keep": false,
                "name": "convert_",
                "src": "hda",
                "tags": []
            }
        ],
        "batch": false
    },
    "inputB": {
        "values": [
            {
                "hid": 72,
                "id": "be2dfb734c2d1ff7",
                "keep": false,
                "name": "convert_",
                "src": "hda",
                "tags": []
            }
        ],
        "batch": false
    },
    "strand": "",
    "overlap_mode": [
        "-wa"
    ],
    "split": "false",
    "fraction": "",
    "reciprocal": "false",
    "invert": "false",
    "once": "false",
    "count": "false",
    "header": "false"
}

}

SO I uninstalled deeptools and bedtools and reinstalled it but the error is not resolved. SO have you any idea to resolve this problem ?

EDIT : Very strange behaviour !!! When I go in "tool lineage" with admin interface and click on the link of the installed tool, the formular appears and I can run the job without error from this interface but cannot rerun it from the "Analyze Data" frame ?! I don't understand what's happen

Thanks

error shed tools update galaxy • 669 views

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modified 14 months ago • written 15 months ago by julie dubois • 20

14 months ago by

danielsauceda • 60

Texas A&M

danielsauceda • 60 wrote:

Yes I have also noticed similar things happening with 17.05. I have to be honest I cannot quite recall the fix. But bear with me

I believe this only happens with the tools install via toolshed. Inside of /galaxy/config/shed_tool_conf.xml each tool is listed like so.

<section id="textutil" name="Text Manipulation" version="">
  <tool file="toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/1cb70a56fc89/datamash_transpose/datamash-transpose.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.0.6">
      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
        <repository_name>datamash_transpose</repository_name>
        <repository_owner>iuc</repository_owner>
        <installed_changeset_revision>1cb70a56fc89</installed_changeset_revision>
        <id>toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.0.6</id>
        <version>1.0.6</version>
    </tool>
</section>

Try deleting the section with guid="toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.0.6" and restart galaxy.

ADD COMMENT • link modified 14 months ago • written 14 months ago by danielsauceda • 60

14 months ago by

julie dubois • 20

julie dubois • 20 wrote:

Hi, THANKS a lot, it was the solution !!!

The mystery is in the fact that not all tools installed with Toolshed are impacted.

Thanks again.

Julie

ADD COMMENT • link written 14 months ago by julie dubois • 20

They really need to fix this lol

ADD REPLY • link written 14 months ago by danielsauceda • 60

14 months ago by

m.vandenbeek • 10

France

m.vandenbeek • 10 wrote:

Please do not edit the shed_tool_conf.xml, this has most likely been fixed in June. If this does not work on a recent commit of the release_17.05 branch please open a bug report, including the commit you are using now. Thanks.

ADD COMMENT • link modified 14 months ago • written 14 months ago by m.vandenbeek • 10

I did but I did fail to update the Bug when you asked more questions. I apologize. Yes I am using APACHE2 and version 17.05

ADD REPLY • link modified 14 months ago • written 14 months ago by danielsauceda • 60

14 months ago by

julie dubois • 20

julie dubois • 20 wrote:

Hi, I've updated to the lastest commit. I'll report bug if it persist.

Thanks

Julie

ADD COMMENT • link written 14 months ago by julie dubois • 20

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