galaxyproject / galaxyproject/galaxy

Toolshed Installed tool : Job submission Failed after upgrading galaxy to 17.05

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Python
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Description

Issue temporarly resolved with help of other user (https://biostar.usegalaxy.org/p/24710/#24766)
Some tools (in my case only bedtools and deeptools, but not samtools for example) installed in my previous version of galaxy with toolshed, fail to run in the new version of galaxy.
The formular is available, but when we execute the job, no entry appears in history and a red pop-up appears with this message :

{
"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"
}
uninstall and reinstall these tools doesn't resolve the problem
resolved by removing "guid=..." in config/shed_tool_conf.xml

Contributor guide

Open the contributing guide

Research direction

Start with config/shed_tool_conf.xml and reproduce the failure for previously installed bedtools or deeptools after upgrading Galaxy to 17.05. Compare behavior with and without the guid entry; done means the affected tools submit jobs and create history entries without manually removing guid or reinstalling them.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
backend
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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