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Add MMseqs2 clustering and taxonomy #6574

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Add MMseqs2 clustering and taxonomy #6574

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Commits on Oct 15, 2024

  1. Init mmseqs2

    @clsiguret
    clsiguret committed Oct 15, 2024
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  2. init DM

    @hugolefeuvre
    hugolefeuvre committed Oct 15, 2024
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Commits on Oct 16, 2024

  1. continue DM

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    hugolefeuvre committed Oct 16, 2024
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  2. Split to TOOL_VERSION and COMMIT

    @clsiguret
    clsiguret committed Oct 16, 2024
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  3. Modify macros and json output

    @hugolefeuvre
    hugolefeuvre committed Oct 16, 2024
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  4. update macro

    @clsiguret
    clsiguret committed Oct 16, 2024
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  5. init mmseqs2_taxonomy

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    clsiguret committed Oct 16, 2024
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  6. init mmseqs2_createtaxdb

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    clsiguret committed Oct 16, 2024
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  7. Change name and description

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    clsiguret committed Oct 16, 2024
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  8. init mmseqs2_createdb

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    clsiguret committed Oct 16, 2024
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  9. init mmseqs2_createtsv

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    clsiguret committed Oct 16, 2024
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  10. init mmseqs2_createtsv

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    clsiguret committed Oct 16, 2024
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  11. Merge branch 'mmseqs2' of github.com:clsiguret/tools-iuc into mmseqs2

    @clsiguret
    clsiguret committed Oct 16, 2024
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  12. continue DM

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    hugolefeuvre committed Oct 16, 2024
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Commits on Oct 17, 2024

  1. init taxonomyreport

    @clsiguret
    clsiguret committed Oct 17, 2024
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  2. add test files for createtsv

    @clsiguret
    clsiguret committed Oct 17, 2024
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  3. Add second test with other data table

    @hugolefeuvre
    hugolefeuvre committed Oct 17, 2024
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  4. add double quote

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    hugolefeuvre committed Oct 17, 2024
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  5. start create_db

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    hugolefeuvre committed Oct 17, 2024
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Commits on Oct 18, 2024

  1. continue mmseqs2 DM (macros modification)

    @hugolefeuvre
    hugolefeuvre committed Oct 18, 2024
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  2. put all xml into one

    @clsiguret
    clsiguret committed Oct 18, 2024
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  3. put all xml into one

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    clsiguret committed Oct 18, 2024
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  4. Merge branch 'galaxyproject:main' into mmseqs2

    @hugolefeuvre
    hugolefeuvre authored Oct 18, 2024
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  5. add createdb section

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    hugolefeuvre committed Oct 18, 2024
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  6. add createtaxdb and filtertaxseqdb sections

    @clsiguret
    clsiguret committed Oct 18, 2024
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  7. Update taxonomy assignement : taxonomy module prefilter options

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    hugolefeuvre committed Oct 18, 2024
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Commits on Oct 21, 2024

  1. taxonomy part : align parameters

    @hugolefeuvre
    hugolefeuvre committed Oct 21, 2024
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Commits on Oct 22, 2024

  1. taxonomy module : misc and common options

    @hugolefeuvre
    hugolefeuvre committed Oct 22, 2024
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Commits on Oct 23, 2024

  1. all parameters into xml

    @hugolefeuvre
    hugolefeuvre committed Oct 23, 2024
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  2. finish wrapping command and start tests

    @hugolefeuvre
    hugolefeuvre committed Oct 23, 2024
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Commits on Oct 24, 2024

  1. Change tool name

    @hugolefeuvre
    hugolefeuvre committed Oct 24, 2024
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Commits on Oct 30, 2024

  1. Merge branch 'galaxyproject:main' into mmseqs2

    @hugolefeuvre
    hugolefeuvre authored Oct 30, 2024
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  2. Merge branch 'mmseqs2_DM' into mmseqs2 

    Merge mmseqs2_DM branch into mmseqs2 branch
    @hugolefeuvre
    hugolefeuvre committed Oct 30, 2024
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  3. add new loc.sample file and modification to pass tests

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    hugolefeuvre committed Oct 30, 2024
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Commits on Oct 31, 2024

  1. issue with database : test dont select test database

    @hugolefeuvre
    hugolefeuvre committed Oct 31, 2024
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Commits on Nov 4, 2024

  1. group multiple conditionnal part

    @hugolefeuvre
    hugolefeuvre committed Nov 4, 2024
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  2. start mmseqs2 easy-linclust wrapper

    @hugolefeuvre
    hugolefeuvre committed Nov 4, 2024
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Commits on Nov 7, 2024

  1. finish mmseqs2 linclust wrapping

    @hugolefeuvre
    hugolefeuvre committed Nov 7, 2024
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  2. start easy-taxo wrapper, I want to compare taxonomy and easy-taxonomy

    @hugolefeuvre
    hugolefeuvre committed Nov 7, 2024
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Commits on Nov 8, 2024

  1. modify easy-taxonomy : conditionnal and resolve DB issue

    @hugolefeuvre
    hugolefeuvre committed Nov 8, 2024
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  2. Merge branch 'galaxyproject:main' into mmseqs2

    @hugolefeuvre
    hugolefeuvre authored Nov 8, 2024
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Commits on Nov 12, 2024

  1. update taxo : issue with mmseqs, update with easy-taxo : issue with i… 

    …nput/output paramaters that are not detected
    @hugolefeuvre
    hugolefeuvre committed Nov 12, 2024
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Commits on Nov 14, 2024

  1. filter kraken or krona output

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    hugolefeuvre committed Nov 14, 2024
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Commits on Nov 15, 2024

  1. start modify DM

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    hugolefeuvre committed Nov 15, 2024
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  2. modify DM path and json informations

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    hugolefeuvre committed Nov 15, 2024
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Commits on Nov 18, 2024

  1. wrong value

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    hugolefeuvre committed Nov 18, 2024
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  2. start multiple datatable management

    @hugolefeuvre
    hugolefeuvre committed Nov 18, 2024
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  3. add nucleotide data table into param

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    hugolefeuvre committed Nov 18, 2024
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Commits on Nov 19, 2024

  1. Reduced database, possibility of having the 2 types of report

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    hugolefeuvre committed Nov 19, 2024
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  2. Merge branch 'galaxyproject:main' into mmseqs2

    @hugolefeuvre
    hugolefeuvre authored Nov 19, 2024
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  3. delete useless files and parameters + last tests

    @hugolefeuvre
    hugolefeuvre committed Nov 19, 2024
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  4. try to chmod Swiss-Prot_taxonomy because error could not open for wri… 

    …ting
    @hugolefeuvre
    hugolefeuvre committed Nov 19, 2024
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Commits on Nov 20, 2024

  1. Create a symlink of the database to the job working directory 

    Ensure that the _taxonomy file is not written to the test data section

Co-authored-by: M Bernt <[email protected]>
    @hugolefeuvre @bernt-matthias
    hugolefeuvre and bernt-matthias authored Nov 20, 2024
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