This document outlines the implementation plan for creating a Galaxy file source plugin that uses Aspera ascp for high-speed file downloads. The implementation will be a configured plugin (not stock) with download-only functionality, using a custom fsspec filesystem.
| { | |
| "@context": "http://schema.org", | |
| "@type": "LearningResource", | |
| "http://purl.org/dc/terms/conformsTo": { | |
| "@id": "https://bioschemas.org/profiles/TrainingMaterial/1.0-RELEASE", | |
| "@type": "CreativeWork" | |
| }, | |
| "audience": { | |
| "@type": "EducationalAudience", | |
| "educationalRole": "Students" |
| ========================================= | |
| Galaxy API Rate Limiting Test (Parallel) | |
| ========================================= | |
| Target: https://test.galaxyproject.org | |
| Endpoint: https://test.galaxyproject.org/api/version | |
| Temp dir: /var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp.9BmqdrrwVf | |
| === Test 1: Burst Capacity Test === | |
| Testing burst capacity with 0c918d2fbb... |
Job failed on first run, rerun with "replace dataset collection elements" selected. Discovered output dataset collection elements were added to original collection, while new output dataset collection is not populated. This probably makes the job ineligible for the job cache / job search.
| #!/usr/bin/env python3 | |
| """ | |
| Benchmarking script for Galaxy API endpoints performance testing. | |
| This script creates a test history with a configurable list:list collection, | |
| then benchmarks two API endpoints: | |
| 1. /api/histories/{history_id}/contents | |
| 2. /api/dataset_collections/{hdca_id}/contents/{collection_id} | |
| """ |
| library(GBCC.mcm) | |
| library(SummarizedExperiment) | |
| library(SpatialFeatureExperiment) | |
| x = GBCC.mcm::process_mcmicro("input.h5ad") | |
| expr_matrix <- assay(x, "X") | |
| expr_df <- as.data.frame(t(expr_matrix)) # Transpose so cells are rows | |
| # Get cell metadata | |
| metadata <- as.data.frame(colData(x)) | |
| # Get spatial coordinates | |
| coords <- as.data.frame(spatialCoords(x)) |
| EXPLAIN (ANALYZE, COSTS, VERBOSE, BUFFERS, FORMAT JSON) SELECT | |
| filtered_jobs_subquery.job_id, | |
| filtered_jobs_subquery."reference_genome|history_item_152775960", | |
| filtered_jobs_subquery."library|input_1_152726579" | |
| FROM | |
| ( | |
| SELECT | |
| job_ids_subquery.job_id AS job_id, | |
| job_ids_subquery."reference_genome|history_item_152775960" AS "reference_genome|history_item_152775960", | |
| job_ids_subquery."library|input_1_152726579" AS "library|input_1_152726579" |
| diff --git a/lib/galaxy/model/migrations/alembic/versions_gxy/0c681a59dce1_add_on_delete_to_fkey_on_event_session_.py b/lib/galaxy/model/migrations/alembic/versions_gxy/0c681a59dce1_add_on_delete_to_fkey_on_event_session_.py | |
| new file mode 100644 | |
| index 00000000000..a449de1b6d7 | |
| --- /dev/null | |
| +++ b/lib/galaxy/model/migrations/alembic/versions_gxy/0c681a59dce1_add_on_delete_to_fkey_on_event_session_.py | |
| @@ -0,0 +1,40 @@ | |
| +"""Add on-delete to fkey on event.session_id | |
| + | |
| +Revision ID: 0c681a59dce1 | |
| +Revises: 24feca8a6a5a |
| { | |
| "$defs": { | |
| "CollectionElementCollectionRequestUri": { | |
| "additionalProperties": false, | |
| "properties": { | |
| "class": { | |
| "const": "Collection", | |
| "title": "Class", | |
| "type": "string" | |
| }, |
| workflows: | |
| - trs_id: '#workflow/github.com/iwc-workflows/assembly-with-flye/main/versions/v0.2' | |
| workflow_categories: | |
| - ASSEMBLY | |
| workflow_name: Genome assembly with Flye | |
| workflow_description: Assemble long reads with Flye, then view assembly statistics | |
| and assembly graph | |
| ploidy: any | |
| parameters: | |
| Input sequence reads: |