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non-canonical intron branch update from master #714
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Commits on Oct 27, 2022
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Lars Gabriel committed
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added missing files to example/results
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Lars Gabriel committed
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removed depricated figures and updated braker3 figure
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minor changes in documentation
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Merge pull request #547 from Gaius-Augustus/master
Update log_reg_prothints.pl to ProtHint's version as suggested in #473
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correcting test3 restart scripts
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Merge branch 'braker3' of https://github.com/Gaius-Augustus/BRAKER in…
…to braker3
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Commits on Nov 14, 2022
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fixed softmasking option for ETP+ call
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adjust augustus paths for singularity
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changed warning message for unwritebale AUGUSTUS_CONFIG_PATH
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Merge branch 'braker3' of https://github.com/Gaius-Augustus/BRAKER in…
…to braker3
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added test for downloading RNA-Seq from SRA
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Lars Gabriel committed
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The dollar at $species was incorrect in line 1892
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adjusted name of genemark-etp executable according to its github version
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change BRAKER3 to fit the updated ETP version
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Merge pull request #578 from Gaius-Augustus/master
Fixing README.md
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Merge pull request #579 from Gaius-Augustus/braker3
Merge pull request #578 from Gaius-Augustus/master
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renamed helpMod.pm to helpMod_braker.pm
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Make it very clear that UTR prediction is not fully functional and sh…
…ould not be used
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remove . at the end of protein sequences
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Merge pull request #583 from Gaius-Augustus/issue_582
remove . at the end of protein sequences
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added RNA-Seq alignment info for BRAKER3
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fixed gtf to gff3 conversion, added ETP preprint citation
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Merge branch 'master' of https://github.com/Gaius-Augustus/BRAKER
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Merge pull request #624 from Gaius-Augustus/gff3_issue
Gff3 issue
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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.
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Merge pull request #661 from Gaius-Augustus/KatharinaHoff-patch-1
Update Dockerfile
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Merge pull request #671 from Gaius-Augustus/KatharinaHoff-patch-2
Update README.md
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adding UTRs seems to work for both single and multi exon genes, but g…
…ene lines are still printed double
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Merge pull request #682 from Gaius-Augustus/braker3
adding Augustus parameters foldr that is missing from Debian package
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reduced verbosity of LOG for fix_in_frame_stop_codon_genes.py
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reduced verbosity of LOG for fix_in_frame_stop_codon_genes.py
Lars Gabriel committedOct 19, 2023 Configuration menu - View commit details
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reduced verbosity of LOG for fix_in_frame_stop_codon_genes.py
Lars Gabriel committedOct 19, 2023 Configuration menu - View commit details
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Merge pull request #689 from Gaius-Augustus/ifs_verbosity
Ifs verbosity
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Commits on Oct 20, 2023
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Lars Gabriel committed
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added gzip support for RNA-Seq reads
Lars Gabriel committedNov 8, 2023 Configuration menu - View commit details
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Merge pull request #697 from Gaius-Augustus/gzip_support
added gzip support for RNA-Seq reads
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Merge branch 'compleasm' of https://github.com/Gaius-Augustus/BRAKER …
…into compleasm
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Merge pull request #727 from Gaius-Augustus/utr_from_stringtie
Utr from stringtie
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Merge pull request #728 from Gaius-Augustus/master
Updating compleasm branch
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Merge pull request #729 from Gaius-Augustus/braker3_devel
renamed helpMod.pm to helpMod_braker.pm
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Merge pull request #730 from Gaius-Augustus/master
updating compleasm branch
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adding protein file by Rayan that may reduce runtime, remains to be t…
…ested whether that will work for all BRAKER modes
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Merge pull request #773 from sanjaysrikakulam/master
remove AUGUSTUS ENV overwrites from Dockerfile
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Confirmed that singularity container does the SRA download
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within set_JAVA_PATH, generalize check for java version and prevent s…
…ubstitutions within awk command
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Merge pull request #796 from douglasgscofield/master
within set_JAVA_PATH, generalize check for java version and prevent substitutions within awk command
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Merge pull request #824 from Gaius-Augustus/fix_compute_acc
fixed pseudo gene removal in evaluation script
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Merge pull request #881 from schloegl/master
fix for using other openjdk java (e.g. Zulu from Azul)
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