Question: Toolshed INstalled tool : Job submission Failed after upgrading galaxy local instance
0
gravatar for julie dubois
15 months ago by
julie dubois20
julie dubois20 wrote:

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

ADD COMMENTlink modified 14 months ago • written 15 months ago by julie dubois20
1
gravatar for danielsauceda
14 months ago by
Texas A&M
danielsauceda60 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 COMMENTlink modified 14 months ago • written 14 months ago by danielsauceda60
1
gravatar for julie dubois
14 months ago by
julie dubois20
julie dubois20 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 COMMENTlink written 14 months ago by julie dubois20

They really need to fix this lol

ADD REPLYlink written 14 months ago by danielsauceda60
1
gravatar for m.vandenbeek
14 months ago by
m.vandenbeek10
France
m.vandenbeek10 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 COMMENTlink modified 14 months ago • written 14 months ago by m.vandenbeek10

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 REPLYlink modified 14 months ago • written 14 months ago by danielsauceda60
0
gravatar for julie dubois
14 months ago by
julie dubois20
julie dubois20 wrote:

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

Thanks

Julie

ADD COMMENTlink written 14 months ago by julie dubois20
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