Add link to IWC (Intergalactic Workflow Commission) curated workflows at https://iwc.galaxyproject.org/ in Galaxy's workflow list interface. Implement BOTH a tab approach and a banner approach so you can decide which works better.
I'm review a PR. It adds this file lib/galaxy/files/sources/omero.py - which is implementing a Galaxy File Source plugins. I'm worried about the size of the file - it seems large and it interwines plugin implementation logic and API communication a lot - would it make sense to extract the API interaction layer out and reduce the size of the plugin or does it make more sense as is?
Based on my analysis, here's my assessment:
Current implementation in wes.py:
_build_task_logs() (lines 886-913): Loads ALL WorkflowInvocationSteps into memory, then all related Jobsget_run_tasks() (line 701) - loads all, slices in Pythonget_run_task() (line 742) - loads all to find one_invocation_to_run_log() (line 868) - populates deprecated field
| Found 4 test cases to validate for tool shasta / 0.6.0+galaxy0 (@ /Users/jxc755/workspace/tools-iuc/tools/shasta/shasta.xml) | |
| Test Case 1: validated | |
| Test Case 2: validated | |
| Test Case 3: validated | |
| Test Case 4: validation failed - Invalid parameter name found kmers|enrichmentThreshold | |
| Found 3 test cases to validate for tool bg_diamond_view / 2.0.8 (@ /Users/jxc755/workspace/tools-iuc/tools/diamond/diamond_view.xml) | |
| Test Case 1: validated | |
| Test Case 2: validated | |
| Test Case 3: validation failed - 1 validation error for DynamicModelForTool | |
| forwardonly |
| toolshed.g2.bx.psu.edu/repos/devteam/cummerbund_to_tabular/cummerbund_to_cuffdiff | |
| toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_coverage_distributions | |
| toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_population_structure |
| Server running... press ctrl-c to stop. | |
| Regenerating: 1 file(s) changed at 2020-07-09 12:50:54 | |
| topics/dev/images/core_plugins_overview.plantuml.txt | |
| Warning: Empty `slug` generated for ''. | |
| Warning: Empty `slug` generated for ''. | |
| [2020-07-09 12:57:05] ERROR Errno::ECONNRESET: Connection reset by peer @ io_fillbuf - fd:17 | |
| /Users/john/miniconda3/envs/galaxy_training_material/lib/ruby/2.4.0/webrick/httpserver.rb:82:in `eof?' | |
| /Users/john/miniconda3/envs/galaxy_training_material/lib/ruby/2.4.0/webrick/httpserver.rb:82:in `run' | |
| /Users/john/miniconda3/envs/galaxy_training_material/lib/ruby/2.4.0/webrick/server.rb:308:in `block in start_thread' |
| >>> import galaxy.tools.parser | |
| >>> import galaxy.tools.parser.factory | |
| >>> tool_source = galaxy.tools.parser.factory.get_tool_source("bwa.xml") | |
| >>> reqs, _ = tool_source.parse_requirements_and_containers() | |
| >>> from galaxy.tools.deps.conda_util import CondaTarget | |
| >>> from galaxy.tools.deps.conda_util import hash_conda_packages | |
| >>> hash_conda_packages([CondaTarget(req.name, req.version) for req in reqs]) | |
| '28bd91abdde0d474ee5121c1db757e2fe25984a7b393b5288912c68b29b67e02' |
| $ mulled-build --recipes-dir ../bioconda-recipes --targets 'samtools=1.3.1,bedtools=2.22' build | |
| ./involucro -v=3 -f /home/john/workspace/galaxy-lib/galaxy/tools/deps/mulled/invfile.lua -set CHANNELS='bioconda,conda-forge,r' -set TEST='true' -set TARGETS='samtools=1.3.1,bedtools=2.22' -set REPO='quay.io/mulled/mulled-v1-a93fa17175d6f093a6423535399b7ad4ac06ceed' build | |
| [Sep 27 15:58:40] DEBU Run file [/home/john/workspace/galaxy-lib/galaxy/tools/deps/mulled/invfile.lua] | |
| [Sep 27 15:58:40] STEP Run image [continuumio/miniconda:latest] with command [[rm -rf /data/dist]] | |
| [Sep 27 15:58:40] DEBU Creating container [step-4ff4f7eeac] | |
| [Sep 27 15:58:40] DEBU Created container [eb5cdfab2b12 step-4ff4f7eeac], starting it | |
| [Sep 27 15:58:40] DEBU Container [eb5cdfab2b12 step-4ff4f7eeac] started, waiting for completion | |
| [Sep 27 15:58:40] DEBU Container [eb5cdfab2b12 step-4ff4f7eeac] completed with exit code [0] as expected | |
| [Sep 27 15:58:40] DEBU Container [eb5cdfab2b12 step-4ff4f7eeac] removed | |
| [Sep 27 15:58:40] STEP Run image [ |
| class: CommandLineTool | |
| cwlVersion: "cwl:draft-3" | |
| baseCommand: python | |
| arguments: | |
| - valueFrom: input.txt | |
| position: 1 | |
| requirements: | |
| - class: CreateFileRequirement | |
| fileDef: | |
| - filename: input.txt |