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Add FragPipe #761

Merged
merged 34 commits into from
Jul 10, 2024
Merged

Add FragPipe #761

merged 34 commits into from
Jul 10, 2024

Commits on Jul 21, 2022

  1. Initial commit of fragpipe wrapper.

    @reid-wagner
    reid-wagner authored and Galaxy User committed Jul 21, 2022
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Commits on Jul 22, 2022

  1. Agree to academic license.

    @reid-wagner
    reid-wagner authored and Galaxy User committed Jul 22, 2022
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  2. Add protein prophet options. Add data type options for sample groups.… 

    … Correct --accept_license flag.
    @reid-wagner
    reid-wagner authored and Galaxy User committed Jul 22, 2022
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Commits on Oct 15, 2022

  1. - Change Galaxy tool version scheme to devX 

    - Add IonQuant path for headless fragpipe
- Populate options for LFQ-MBR workflow
- Add data_type option for scan inputs
- Make isotope_error a selection option
    @reid-wagner
    reid-wagner authored and Galaxy User committed Oct 15, 2022
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Commits on Nov 18, 2022

  1. Add decoy and contaminant generation.

    @reid-wagner
    reid-wagner committed Nov 18, 2022
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Commits on May 3, 2023

  1. Merge remote-tracking branch 'origin/master' into add_fragpipe

    @reid-wagner
    reid-wagner committed May 3, 2023
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Commits on May 10, 2023

  1. Current progress, including TMT11.

    @reid-wagner
    reid-wagner committed May 10, 2023
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  2. Merge remote-tracking branch 'reid-wagner/add_fragpipe' into add_frag… 

    …pipe
    @reid-wagner
    reid-wagner committed May 10, 2023
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Commits on May 11, 2024

  1. Final edits for release.

    @reid-wagner
    reid-wagner committed May 11, 2024
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Commits on Jun 10, 2024

  1. Merge branch 'master' into add_fragpipe

    @reid-wagner
    reid-wagner authored Jun 10, 2024
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Commits on Jun 14, 2024

  1. Add /usr/local/lib to LD_LIBRARY_PATH for biocontainer environments.

    @reid-wagner
    reid-wagner committed Jun 14, 2024
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  2. Fix tabs in tests.

    @reid-wagner
    reid-wagner committed Jun 14, 2024
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Commits on Jun 26, 2024

  1. Genericize database line-by-line instead of buffering it entirely in … 

    …memory.
    @reid-wagner
    reid-wagner committed Jun 26, 2024
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  2. Remove input scan format conditional.

    @reid-wagner
    reid-wagner committed Jun 26, 2024
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Commits on Jun 27, 2024

  1. Remove -Xmx. FragPipe has its own memory flag.

    @reid-wagner
    reid-wagner committed Jun 27, 2024
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  2. Remove comment and indent.

    @reid-wagner
    reid-wagner committed Jun 27, 2024
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  3. Use a common name for the database, whether it has decoys/contaminant… 

    …s or now, so that a sed replace of workflow file isn't necessary.
    @reid-wagner
    reid-wagner committed Jun 27, 2024
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  4. Make <command> tag easier to follow. Break components into further ma… 

    …cros.
    @reid-wagner
    reid-wagner committed Jun 27, 2024
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  5. Simplify creation of combined_outputs directory.

    @reid-wagner
    reid-wagner committed Jun 27, 2024
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Commits on Jun 29, 2024

  1. Standardize templating formatting.

    @reid-wagner
    reid-wagner committed Jun 29, 2024
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  2. Disable Thermo.raw inputs until mono can be incorporated.

    @reid-wagner
    reid-wagner committed Jun 29, 2024
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  3. Use GALAXY_SLOTS for FragPipe --threads argument.

    @reid-wagner
    reid-wagner committed Jun 29, 2024
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  4. Add profile attribute to tool.

    @reid-wagner
    reid-wagner committed Jun 29, 2024
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  5. Lower profile version to 20.05.

    @reid-wagner
    reid-wagner committed Jun 29, 2024
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  6. Create links to FragPipe installation files in $CONDA_PREFIX. Because… 

    … FragPipe creates cache relative to the lib location, this allows a local FragPipe cache.
    @reid-wagner
    reid-wagner committed Jun 29, 2024
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Commits on Jul 5, 2024

  1. Copy all FragPipe files from conda install locally.

    @reid-wagner
    reid-wagner committed Jul 5, 2024
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  2. Remove unused CWD cheetah variable.

    @reid-wagner
    reid-wagner committed Jul 5, 2024
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  3. Use non-forward slash delimiter. 

    Co-authored-by: M Bernt <[email protected]>
    @reid-wagner @bernt-matthias
    reid-wagner and bernt-matthias authored Jul 5, 2024
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  4. Revert "Use non-forward slash delimiter." 

    Temporarily reverting because this change doesn't pass tests.
    @reid-wagner
    reid-wagner committed Jul 5, 2024
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Commits on Jul 6, 2024

  1. Add wildcard to output data element for log.

    @reid-wagner
    reid-wagner committed Jul 6, 2024
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Commits on Jul 8, 2024

  1. Fix two bugs: isobaric quant user options not included in workflow, a… 

    …nd use_glycan_composition accessed incorrectly.
    @reid-wagner
    reid-wagner committed Jul 8, 2024
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Commits on Jul 9, 2024

  1. Standardize command substitution syntax.

    @reid-wagner
    reid-wagner committed Jul 9, 2024
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  2. Remove CONDA_PREFIX references.

    @reid-wagner
    reid-wagner committed Jul 9, 2024
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  3. Use @ delimiter in sed expressions.

    @reid-wagner
    reid-wagner committed Jul 9, 2024
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