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scottcain / galaxy-workflow-execution-analysis.md
Last active February 17, 2026 21:30
Claude generated details of issues with using Galaxy API and workflow execution

Galaxy Workflow Execution Behavior Analysis

Note: All API calls in this document use [YOUR_API_KEY] as a placeholder. Replace this with your actual Galaxy API key when reproducing these calls.

Issue Summary

When invoking workflows via Galaxy API with a specified target history, workflows consistently create new histories instead of executing in the specified target history. This occurs even with user-owned (imported) workflows, not just public workflows.

Context

@scottcain
scottcain / wall-config.json
Last active February 23, 2026 14:27
wall-config.json
{
"servers": [
"mastodon.social",
"mstdn.science"
],
"tags": [
"galaxyproject",
"galaxyinresearch",
"usegalaxy"
],
@scottcain
scottcain / gist:f0c3575ea042767cb3f6d7ae592947fd
Created February 6, 2024 23:18
start of nclist lf-1.json
[[0,0,230218,0,"NCBI:BK006935.2","chrI","chrI","chrI","SGD","chromosome",
{"Sublist":
[[1,0,801,-1,"SGD:S000028862","SGD:S000028862",
"Telomeric region on the left arm of Chromosome I", "TEL01L","TEL01L","Telomeric region on the left arm of Chromosome I; composed of an X element core sequence, X element combinatorial repeats, and a short terminal stretch of telomeric repeats","chrI","SGD",
[{"end":"801","name":"TEL01L_X_element","seq_id":"chrI","source":"SGD","start":"337","strand":"-","type":"X_element"},
{"end":"336","name":"TEL01L_X_element_combinatorial_repeat","seq_id":"chrI","source":"SGD","start":"63","strand":"-","type":"X_element_combinatorial_repeat"},
{"end":"62","name":"TEL01L_telomeric_repeat_1","seq_id":"chrI","source":"SGD","start":"1","strand":"-","type":"telomeric_repeat"},
{"end":"801","id":"TEL01L_telomere","name":"TEL01L_telomere","seq_id":"chrI","source":"SGD","start":"1","strand":"-","type":"telomere"}],
@scottcain
scottcain / c_elegans protein annotations.gff
Created December 12, 2023 23:28
sample of protein coordinate GFF for C. elegans
###
Y34D9B.1b WormBase polypeptide 1 529 . . . ID=Y34D9B.1b;uniprot_id=Q9N532;wormbase_geneid=WBGene00003238;wormbase_genename=mig-1;wormbase_protein=CE24204
Y34D9B.1b WormBase CDS 1 529 . . . ID=Y34D9B.1b_exon_boundaries;uniprot_id=Q9N532;wormbase_geneid=WBGene00003238;wormbase_genename=mig-1;wormbase_protein=CE24204
Y34D9B.1b WormBase exon 1 43 . . . Parent=Y34D9B.1b_exon_boundaries
Y34D9B.1b WormBase exon 43 90 . . . Parent=Y34D9B.1b_exon_boundaries
Y34D9B.1b WormBase exon 91 161 . . . Parent=Y34D9B.1b_exon_boundaries
Y34D9B.1b WormBase exon 162 208 . . . Parent=Y34D9B.1b_exon_boundaries
Y34D9B.1b WormBase exon 209 239 . . . Parent=Y34D9B.1b_exon_boundaries
Y34D9B.1b WormBase exon 239 2
@scottcain
scottcain / failed seqpanel build
Created November 28, 2023 04:28
failed seqpanel build
(base) MacBook-Pro-6:tmp cain$ git clone https://github.com/scottcain/seqpanel.git
Cloning into 'seqpanel'...
remote: Enumerating objects: 709, done.
remote: Counting objects: 100% (106/106), done.
remote: Compressing objects: 100% (52/52), done.
remote: Total 709 (delta 59), reused 70 (delta 52), pack-reused 603
Receiving objects: 100% (709/709), 2.09 MiB | 3.73 MiB/s, done.
Resolving deltas: 100% (402/402), done.
(base) MacBook-Pro-6:tmp cain$ cd seqpanel/lib
(base) MacBook-Pro-6:lib cain$ yarn
@scottcain
scottcain / bounce email for scottca.in
Created July 20, 2023 18:37
Delivered-To: cain.cshl@gmail.com
Received: by 2002:a17:906:b28f:b0:997:d052:1521 with SMTP id q15csp2320014ejz;
Thu, 20 Jul 2023 11:23:56 -0700 (PDT)
X-Received: by 2002:a17:906:2086:b0:992:387:44d1 with SMTP id 6-20020a170906208600b00992038744d1mr10559686ejq.7.1689877436292;
Thu, 20 Jul 2023 11:23:56 -0700 (PDT)
ARC-Seal: i=1; a=rsa-sha256; t=1689877436; cv=none;
d=google.com; s=arc-20160816;
b=IT7V4jo8D9BrWIAVXBS9We0z+BGfnrPNwjBoqiZUQe0KUxTjkN7if6q5bQaedXFv8t
rxFU3CAfCURBDoqPBHIhMyuYYqWNWN2q1kAIStYCfpQ1tE0mu7bIFI8jzhKF9ca+/FcH
vMDes1pKfi7sPAR9ZoRJq9XkcrmC+KP5pVK1Th2gmrjnoe2fGseoCtyu3+BNlYz36cKX
@scottcain
scottcain / synteny configs
Last active December 1, 2022 04:36
{
"type": "SyntenyTrack",
"trackId": "c_elegans.c_brenneri.paf-1669841807246",
"name": "c_elegans.c_brenneri.paf",
"assemblyNames": [
"c_elegans_PRJNA13758",
"c_brenneri_PRJNA20035"
],
"adapter": {
"type": "PAFAdapter",
@scottcain
scottcain / scratch.js
Last active October 11, 2022 20:03
scottca.in node 4 source
<script src="https://unpkg.com/react@16/umd/react.development.js" crossorigin></script><script src="https://unpkg.com/react-dom@16/umd/react-dom.development.js" crossorigin></script><script src="https://unpkg.com/@jbrowse/react-linear-genome-view/dist/react-linear-genome-view.umd.development.js" crossorigin></script>
<p>We're using the JBrowse Linear Genome View!</p>
<div id="jbrowse2_linear_genome_view" width="500px">this is where the browser should be</div>
<script>
function create_jbrowse2() {
const { createElement } = React
const { render } = ReactDOM
@scottcain
scottcain / LGVembed.js
Last active October 4, 2022 02:28
working LGV in drupal test site but not staging.wormbase.org
//this exact JS works just fine at http://scottca.in/node/3
// but at https://staging.wormbase.org/species/c_elegans/gene/WBGene00001340#09f6--10
// the exact same JS (with an extra fetch to get the releaseVersion) nearly entirely
// works but does NOT offset the track labels--that is the only difference.
//
// Weird
<script src="https://unpkg.com/react@16/umd/react.development.js" crossorigin></script><script src="https://unpkg.com/react-dom@16/umd/react-dom.development.js" crossorigin></script><script src="https://unpkg.com/@jbrowse/react-linear-genome-view/dist/react-linear-genome-view.umd.development.js" crossorigin></script>
function create_jbrowse2() {
@scottcain
scottcain / config.json
Created June 24, 2022 22:06
possible config.json
{
"exports" : {
"c_elegans_PRJNA13758_assembly" : "./c_elegans_PRJNA13758_assembly.js"
}
}