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galaxyproject / training-material

A collection of Galaxy-related training material
https://training.galaxyproject.org
MIT License
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Workflows with tools not in toolshed #1710

Open bedroesb opened 4 years ago

bedroesb commented 4 years ago

As a followup on my PR #1709, there were tools in workflows I could not attach the correct tool_shed_repository to:

Topic Tutorial Tutorial name Tutorial file name Tool name [Tool id] that does not exist in toolshed
proteomics secretome-prediction Secreted Proteins via GO annotation and WoLF PSORT for shCTSB paper WF_secretomePrediction_goWolfpsort.ga Get all the term IDs and term names of a given OBO ontology[term_id_vs_term_name], Get subontology from a given OBO term[get_subontology_from]
~computational-chemistry~ ~cheminformatics~ ~CTB workflow~ ~main_workflow.ga~ ~NxN Clustering[testtoolshed.g2.bx.psu.edu/repos/bgruening/chemfp/ctb_chemfp_nxn_clustering/0.1], Remove duplicated molecules[testtoolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_remDuplicates/1.0], Compound Search[testtoolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_obgrep/0.1], Natural Product[testtoolshed.g2.bx.psu.edu/repos/bgruening/natural_product_likeness/ctb_np-likeness-calculator/0.1], Compound Convert[testtoolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_compound_convert/0.1], Remove counterions and fragments[testtoolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_remIons/1.0], Change Title[testtoolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_change_title/0.0.1]~
computational-chemistry md-simulation-namd MD_NAMD main_workflow.ga NAMD MD Simulator (NPT)[namd_npt], Energy Minimizer[minimizer], NAMD MD Simulator (NVT)[namd_nvt], System Setup[setup]
computational-chemistry md-simulation-namd NAMD_MD_from_CHARMM-GUI main_workflow_charmmgui.ga NAMD MD Simulator (NPT)[namd_npt], NAMD MD Simulator (NVT)[namd_nvt]

The second one is off course because they are still in the test tool shed.

hexylena commented 4 years ago

I've meant to setup a PR test that prevents workflows with TTS tools from being committed. Could also be an easy task for someone :)

hexylena commented 4 years ago

fixed with new linting.

bedroesb commented 4 years ago

@hexylena I don't know if the others from computational chemistry and proteomics are already fixed? Because they do not contain tools from the test toolshed, but they do also not have "tool_shed_repository" attribute, and because of that are not recognized by Workflow-to-tools from ephemeris

hexylena commented 4 years ago

Something else to lint on!

hexylena commented 1 year ago

No longer an issue! (meaning added to the linting, but, ugh, yeah, ok, comp chem still not updated.)