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non-canonical intron branch update from master #714

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Commits on Oct 27, 2022

  1. update example results

    Lars Gabriel committed Oct 27, 2022
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  2. added missing files to example/results

    Lars Gabriel committed Oct 27, 2022
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  3. update braker3 flowchart

    Lars Gabriel committed Oct 27, 2022
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  4. moved figure to correct place

    Lars Gabriel committed Oct 27, 2022
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  5. Delete braker3_etp.png

    LarsGab authored Oct 27, 2022
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  6. Add files via upload

    LarsGab authored Oct 27, 2022
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Commits on Nov 1, 2022

  1. minor changes

    Lars Gabriel committed Nov 1, 2022
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  2. removed depricated figures and updated braker3 figure

    Lars Gabriel committed Nov 1, 2022
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  3. Add files via upload

    LarsGab authored Nov 1, 2022
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Commits on Nov 2, 2022

  1. Revert "Add files via upload"

    This reverts commit 6eea185.
    LarsGab committed Nov 2, 2022
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  2. minor changes in documentation

    Lars Gabriel committed Nov 2, 2022
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Commits on Nov 7, 2022

  1. Update README.md

    KatharinaHoff authored Nov 7, 2022
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  2. updated README

    KatharinaHoff committed Nov 7, 2022
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  10. updated README.braker

    KatharinaHoff committed Nov 7, 2022
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  12. updated README

    KatharinaHoff committed Nov 7, 2022
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  14. always set_TSEBRA_PATH

    KatharinaHoff committed Nov 7, 2022
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  16. Merge pull request #547 from Gaius-Augustus/master

    Update log_reg_prothints.pl to ProtHint's version as suggested in #473
    LarsGab authored Nov 7, 2022
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  22. adding skipOptimize

    KatharinaHoff committed Nov 7, 2022
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  25. removing print

    KatharinaHoff committed Nov 7, 2022
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  26. adding skipOptimize

    KatharinaHoff committed Nov 7, 2022
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  29. correcting test3 restart scripts

    Lars Gabriel committed Nov 7, 2022
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  30. Merge branch 'braker3' of https://github.com/Gaius-Augustus/BRAKER in…

    …to braker3
    Lars Gabriel committed Nov 7, 2022
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Commits on Nov 14, 2022

  1. fixed softmasking option for ETP+ call

    Lars Gabriel committed Nov 14, 2022
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Commits on Nov 16, 2022

  1. adjust augustus paths for singularity

    Lars Gabriel committed Nov 16, 2022
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Commits on Nov 21, 2022

  1. Update braker.pl

    KatharinaHoff authored Nov 21, 2022
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Commits on Dec 16, 2022

  1. Update README.md

    KatharinaHoff authored Dec 16, 2022
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  2. Update README.md

    KatharinaHoff authored Dec 16, 2022
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Commits on Jan 5, 2023

  1. Update README.md

    KatharinaHoff authored Jan 5, 2023
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  2. Update README.md

    KatharinaHoff authored Jan 5, 2023
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  3. Update README.md

    KatharinaHoff authored Jan 5, 2023
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  4. Update README.md

    KatharinaHoff authored Jan 5, 2023
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  5. Update README.md

    KatharinaHoff authored Jan 5, 2023
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Commits on Jan 11, 2023

  1. find correct path of perl

    Lars Gabriel committed Jan 11, 2023
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  2. Merge branch 'braker3' of https://github.com/Gaius-Augustus/BRAKER in…

    …to braker3
    Lars Gabriel committed Jan 11, 2023
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  3. added test for downloading RNA-Seq from SRA

    Lars Gabriel committed Jan 11, 2023
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  4. Update README.md

    LarsGab authored Jan 11, 2023
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  5. results of test3_4

    Lars Gabriel committed Jan 11, 2023
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  6. Add files via upload

    LarsGab authored Jan 11, 2023
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  7. Update README.md

    LarsGab authored Jan 11, 2023
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  8. Update print_braker3_setup.py

    use /usr/bin/perl in container
    KatharinaHoff authored Jan 11, 2023
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  9. Update braker.pl

    The dollar at $species was incorrect in line 1892
    KatharinaHoff authored Jan 11, 2023
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Commits on Jan 12, 2023

  1. wrong branch

    KatharinaHoff committed Jan 12, 2023
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  3. BRAKER2 test

    KatharinaHoff committed Jan 12, 2023
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  4. testing BRAKER3

    KatharinaHoff committed Jan 12, 2023
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  6. Update test1.sh

    KatharinaHoff authored Jan 12, 2023
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  7. Update test2.sh

    KatharinaHoff authored Jan 12, 2023
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  8. Update test3.sh

    KatharinaHoff authored Jan 12, 2023
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  9. Create Dockerfile

    KatharinaHoff authored Jan 12, 2023
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  10. Update README.md

    KatharinaHoff authored Jan 12, 2023
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Commits on Jan 15, 2023

  1. Merge pull request #561 from Gaius-Augustus/pag30

    Update README.md
    LarsGab authored Jan 15, 2023
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  2. Update README.md

    LarsGab authored Jan 15, 2023
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  3. Update README.md

    LarsGab authored Jan 15, 2023
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Commits on Jan 18, 2023

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  2. Update README.md

    LarsGab authored Jan 18, 2023
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Commits on Jan 20, 2023

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  2. Update test1.sh

    KatharinaHoff authored Jan 20, 2023
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  3. Update test2.sh

    KatharinaHoff authored Jan 20, 2023
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  4. Update test3.sh

    KatharinaHoff authored Jan 20, 2023
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Commits on Jan 25, 2023

  1. Add files via upload

    LarsGab authored Jan 25, 2023
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  2. Add files via upload

    LarsGab authored Jan 25, 2023
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Commits on Feb 2, 2023

  1. Update README.md

    LarsGab authored Feb 2, 2023
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Commits on Feb 7, 2023

  1. Update README.md

    LarsGab authored Feb 7, 2023
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Commits on Mar 1, 2023

  1. change BRAKER3 to fit the updated ETP version

    Lars Gabriel committed Mar 1, 2023
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  2. Update test3.sh

    removed MakeHub
    LarsGab authored Mar 1, 2023
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  3. Update test3_4.sh

    LarsGab authored Mar 1, 2023
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  4. Update README.md

    LarsGab authored Mar 1, 2023
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  5. update test results

    Lars Gabriel committed Mar 1, 2023
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  6. update Singularity tests

    Lars Gabriel committed Mar 1, 2023
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Commits on Mar 2, 2023

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  3. Merge pull request #578 from Gaius-Augustus/master

    Fixing README.md
    KatharinaHoff authored Mar 2, 2023
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  4. Update README.md

    KatharinaHoff authored Mar 2, 2023
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  6. Merge pull request #579 from Gaius-Augustus/braker3

    Merge pull request #578 from Gaius-Augustus/master
    KatharinaHoff authored Mar 2, 2023
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  7. Update README.md

    KatharinaHoff authored Mar 2, 2023
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  8. Update braker.pl

    Make warning look prettier
    KatharinaHoff authored Mar 2, 2023
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  10. Update README.md

    KatharinaHoff authored Mar 2, 2023
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  11. Update README.md

    KatharinaHoff authored Mar 2, 2023
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  12. Update README.md

    KatharinaHoff authored Mar 2, 2023
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  13. Update README.md

    KatharinaHoff authored Mar 2, 2023
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  14. Update braker.pl

    KatharinaHoff authored Mar 2, 2023
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  15. Update braker.pl

    KatharinaHoff authored Mar 2, 2023
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Commits on Mar 3, 2023

  1. renamed helpMod.pm to helpMod_braker.pm

    Lars Gabriel committed Mar 3, 2023
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Commits on Mar 4, 2023

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  3. Update README.md

    KatharinaHoff authored Mar 4, 2023
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  4. Update README.md

    KatharinaHoff authored Mar 4, 2023
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  5. Update braker.pl

    KatharinaHoff authored Mar 4, 2023
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Commits on Mar 5, 2023

  1. Update README.md

    KatharinaHoff authored Mar 5, 2023
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Commits on Mar 6, 2023

  1. remove . at the end of protein sequences

    Lars Gabriel committed Mar 6, 2023
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  2. Merge pull request #583 from Gaius-Augustus/issue_582

    remove . at the end of protein sequences
    LarsGab authored Mar 6, 2023
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Commits on Mar 9, 2023

  1. added RNA-Seq alignment info for BRAKER3

    Lars Gabriel committed Mar 9, 2023
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Commits on Mar 31, 2023

  1. Update README.md

    KatharinaHoff authored Mar 31, 2023
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  2. Update README.md

    KatharinaHoff authored Mar 31, 2023
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Commits on Apr 25, 2023

  1. Update README.md

    fixed link
    MarioStanke authored Apr 25, 2023
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  2. fixed gtf to gff3 conversion, added ETP preprint citation

    Lars Gabriel committed Apr 25, 2023
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Commits on Apr 29, 2023

  1. Update README.md

    typo: per-partitioned -> pre-partitioned
    MarioStanke authored Apr 29, 2023
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Commits on Jun 23, 2023

  1. users suggested to change the java version check line in braker.pl ; …

    …we are not actively maintaining this part of the pipeline at the moment, but I committed the change, either way. Not tested.
    KatharinaHoff committed Jun 23, 2023
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Commits on Jul 8, 2023

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Commits on Aug 22, 2023

  1. Update Dockerfile

    cleaning up old install instructions
    KatharinaHoff authored Aug 22, 2023
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  2. Merge pull request #661 from Gaius-Augustus/KatharinaHoff-patch-1

    Update Dockerfile
    LarsGab authored Aug 22, 2023
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Commits on Sep 18, 2023

  1. Update README.md

    KatharinaHoff authored Sep 18, 2023
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Commits on Sep 22, 2023

  1. Update README.md

    Adding youtube link
    KatharinaHoff authored Sep 22, 2023
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Commits on Sep 25, 2023

  1. Update README.md

    KatharinaHoff authored Sep 25, 2023
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Commits on Sep 28, 2023

  1. fixing #675

    KatharinaHoff committed Sep 28, 2023
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  3. file transfer

    KatharinaHoff committed Sep 28, 2023
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  4. dummy script

    KatharinaHoff committed Sep 28, 2023
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Commits on Sep 29, 2023

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  2. adding UTRs seems to work for both single and multi exon genes, but g…

    …ene lines are still printed double
    KatharinaHoff committed Sep 29, 2023
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  5. fixing a comment

    KatharinaHoff committed Sep 29, 2023
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Commits on Oct 2, 2023

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Commits on Oct 11, 2023

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  2. Merge pull request #682 from Gaius-Augustus/braker3

    adding Augustus parameters foldr that is missing from Debian package
    LarsGab authored Oct 11, 2023
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Commits on Oct 16, 2023

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Commits on Oct 19, 2023

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Commits on Oct 20, 2023

  1. fixed bug in skipGeneMarkETP

    Lars Gabriel committed Oct 20, 2023
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Commits on Oct 21, 2023

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Commits on Nov 7, 2023

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  3. updated version number

    KatharinaHoff committed Nov 7, 2023
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Commits on Nov 8, 2023

  1. added gzip support for RNA-Seq reads

    Lars Gabriel committed Nov 8, 2023
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  2. Merge pull request #697 from Gaius-Augustus/gzip_support

    added gzip support for RNA-Seq reads
    KatharinaHoff authored Nov 8, 2023
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Commits on Nov 9, 2023

  1. Update braker.pl

    KatharinaHoff authored Nov 9, 2023
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Commits on Nov 14, 2023

  1. fixed issue #669

    Lars Gabriel committed Nov 14, 2023
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  3. Update braker.pl

    KatharinaHoff authored Nov 14, 2023
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Commits on Nov 16, 2023

  1. Update braker.pl

    KatharinaHoff authored Nov 16, 2023
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Commits on Nov 20, 2023

  1. Update README.md

    Replaced GeneMark-EX by GeneMark-ES/ET/EP/ETP
    KatharinaHoff authored Nov 20, 2023
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  2. Update README.md

    KatharinaHoff authored Nov 20, 2023
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Commits on Nov 27, 2023

  1. Update README.md

    KatharinaHoff authored Nov 27, 2023
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Commits on Nov 28, 2023

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  2. Update README.md

    KatharinaHoff authored Nov 28, 2023
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Commits on Dec 4, 2023

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Commits on Dec 18, 2023

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Commits on Dec 22, 2023

  1. all changes

    KatharinaHoff committed Dec 22, 2023
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  3. addressing issue #627

    KatharinaHoff committed Dec 22, 2023
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  5. Merge pull request #728 from Gaius-Augustus/master

    Updating compleasm branch
    KatharinaHoff authored Dec 22, 2023
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  6. addressing issue #635

    KatharinaHoff committed Dec 22, 2023
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  7. Merge pull request #729 from Gaius-Augustus/braker3_devel

    renamed helpMod.pm to helpMod_braker.pm
    KatharinaHoff authored Dec 22, 2023
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  8. Merge pull request #730 from Gaius-Augustus/master

    updating compleasm branch
    KatharinaHoff authored Dec 22, 2023
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Commits on Dec 23, 2023

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Commits on Dec 27, 2023

  1. not deleting bbc folder

    KatharinaHoff committed Dec 27, 2023
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  3. adding decision figure

    KatharinaHoff committed Dec 27, 2023
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  4. fixing typo

    KatharinaHoff committed Dec 27, 2023
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Commits on Dec 30, 2023

  1. updates

    KatharinaHoff committed Dec 30, 2023
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  2. Update README.md

    KatharinaHoff authored Dec 30, 2023
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Commits on Jan 6, 2024

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  4. adding protein file by Rayan that may reduce runtime, remains to be t…

    …ested whether that will work for all BRAKER modes
    KatharinaHoff committed Jan 6, 2024
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Commits on Jan 12, 2024

  1. improving documentation

    KatharinaHoff committed Jan 12, 2024
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  2. improving documentation

    KatharinaHoff committed Jan 12, 2024
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  3. improving documentation

    KatharinaHoff committed Jan 12, 2024
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  4. improving documentation

    KatharinaHoff committed Jan 12, 2024
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Commits on Jan 18, 2024

  1. Adding PAG poster

    KatharinaHoff authored Jan 18, 2024
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  2. adding slides from PAG

    KatharinaHoff authored Jan 18, 2024
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Commits on Feb 17, 2024

  1. fixing issue #753

    KatharinaHoff committed Feb 17, 2024
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  2. fixing issue #753

    KatharinaHoff committed Feb 17, 2024
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  4. Update README.md

    KatharinaHoff authored Feb 17, 2024
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  5. Update README.md

    KatharinaHoff authored Feb 17, 2024
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  6. Update README.md

    KatharinaHoff authored Feb 17, 2024
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  7. updating Dockerfile

    KatharinaHoff committed Feb 17, 2024
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Commits on Feb 27, 2024

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  2. Merge pull request #773 from sanjaysrikakulam/master

    remove AUGUSTUS ENV overwrites from Dockerfile
    KatharinaHoff authored Feb 27, 2024
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  3. Update README.md

    KatharinaHoff authored Feb 27, 2024
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  4. Update README.md

    KatharinaHoff authored Feb 27, 2024
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  5. Update README.md

    KatharinaHoff authored Feb 27, 2024
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  6. Update README.md

    KatharinaHoff authored Feb 27, 2024
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  7. Update README.md

    KatharinaHoff authored Feb 27, 2024
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Commits on Mar 14, 2024

  1. Update README.md

    Confirmed that singularity container does the SRA download
    KatharinaHoff authored Mar 14, 2024
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Commits on Mar 27, 2024

  1. Update braker.pl

    Fixing issue #782
    KatharinaHoff authored Mar 27, 2024
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Commits on Mar 30, 2024

  1. updated references

    KatharinaHoff committed Mar 30, 2024
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Commits on Apr 4, 2024

  1. within set_JAVA_PATH, generalize check for java version and prevent s…

    …ubstitutions within awk command
    douglasgscofield committed Apr 4, 2024
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Commits on Apr 26, 2024

  1. Update README.md

    KatharinaHoff authored Apr 26, 2024
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Commits on May 10, 2024

  1. Merge pull request #796 from douglasgscofield/master

    within set_JAVA_PATH, generalize check for java version and prevent substitutions within awk command
    KatharinaHoff authored May 10, 2024
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Commits on May 13, 2024

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  2. Merge pull request #824 from Gaius-Augustus/fix_compute_acc

    fixed pseudo gene removal in evaluation script
    KatharinaHoff authored May 13, 2024
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Commits on Nov 5, 2024

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  2. Merge pull request #881 from schloegl/master

    fix for using other openjdk java (e.g. Zulu from Azul)
    KatharinaHoff authored Nov 5, 2024
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Commits on Nov 14, 2024

  1. Update README.md

    added link to odb12 sets
    KatharinaHoff authored Nov 14, 2024
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  2. Update README.md

    KatharinaHoff authored Nov 14, 2024
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