Open davidchristiany opened 4 years ago
mvdbeek
commented
4 years ago Make sure you connect all input datasets. The UI just fills in a compatible datasets, this doesn't work when running a workflow through the API. If that's not it, can you post the workflow in question ?
davidchristiany
commented
4 years ago Yes I connected all input datasets, it is correcty uploaded in the step 0 and 1, the step 2 cause an error and use the dataset uploaded in step 0:
"steps": {
"0": {
"annotation": "",
"content_id": null,
"errors": null,
"id": 0,
"input_connections": {},
"inputs": [
{
"description": "",
"name": "wt_H3K4me3_read1.fastqsanger"
}
],
"label": "R1",
"name": "Input dataset",
"outputs": [],
"position": {
"left": 204,
"top": 333
},
"tool_id": null,
"tool_state": "{\"name\": \"reads_1\"}",
"tool_version": null,
"type": "data_input",
"uuid": "71f77373-c9b8-441c-bbf3-b168fbb69220",
"workflow_outputs": [
{
"label": null,
"output_name": "output",
"uuid": "84ca7fba-f3a1-4b15-9d20-ce6468a0bd35"
}
]
},
"1": {
"annotation": "",
"content_id": null,
"errors": null,
"id": 1,
"input_connections": {},
"inputs": [
{
"description": "",
"name": "wt_H3K4me3_read2.fastqsanger"
}
],
"label": "R2",
"name": "Input dataset",
"outputs": [],
"position": {
"left": 200,
"top": 458
},
"tool_id": null,
"tool_state": "{\"name\": \"reads_2\"}",
"tool_version": null,
"type": "data_input",
"uuid": "3da9f126-0edf-4243-88f7-e1d1528840f6",
"workflow_outputs": [
{
"label": null,
"output_name": "output",
"uuid": "93a3c29c-fab2-407b-87dd-e49758644ddf"
}
]
},
"2": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
"errors": null,
"id": 2,
"input_connections": {
"input_file": {
"id": 0,
"output_name": "output"
}
},
"inputs": [
{
"description": "runtime parameter for tool FastQC",
"name": "limits"
},
{
"description": "runtime parameter for tool FastQC",
"name": "contaminants"
},
{
"description": "runtime parameter for tool FastQC",
"name": "adapters"
}
],
"label": null,
"name": "FastQC",
"outputs": [
{
"name": "html_file",
"type": "html"
},
{
"name": "text_file",
"type": "txt"
}
],
"position": {
"left": 608,
"top": 147
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
"tool_shed_repository": {
"changeset_revision": "e7b2202befea",
"name": "fastqc",
"owner": "devteam",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"min_length\": \"\\\"\\\"\", \"kmers\": \"\\\"7\\\"\", \"limits\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"input_file\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"__page__\": null, \"adapters\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"contaminants\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"chromInfo\": \"\\\"/usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"nogroup\": \"\\\"false\\\"\"}",
"tool_version": "0.72+galaxy1",
"type": "tool",
"uuid": "003a08a2-3374-4d21-ac16-37e98704ef43",
"workflow_outputs": [
{
"label": null,
"output_name": "html_file",
"uuid": "06217b29-26ad-458f-9892-fca118ab0aa8"
},
{
"label": null,
"output_name": "text_file",
"uuid": "3a7cf686-5c98-45db-91c6-fef52f874201"
}
]
},
I am running several workflows with planemo (version 0.70.0) on a Galaxy instance (20.01). For most of my workflows, it works fine but for some, I didn't find why, only some of the jobs are executed or only inputs datasets are uploaded after that, nothing happens and planemo is waiting forever. I got the following error in galaxy handler logs when it happens:
When I run the same workflow from Galaxy interface it works, but not when I run it from planemo.