AlexanderLabWHOI/EUKulele

Issues

• Improve DB download option

  #65 opened 3 months ago by paulzierep
  2

• EUKulele v2.0.7 fails taxonomy estimation step

  #60 opened 16 days ago by danilodileo
  1

• Visualization Error

  #40 opened 17 days ago by MichielPerneel
  2

• Cant install from Mamba

  #52 opened 17 days ago by blsteven
  5

• No samples found in sample directory with specified peptide extension.

  #59 opened 17 days ago by shibormi
  6

• Mamba install for eukulele=2.0.7 is problematic

  #63 opened 17 days ago by g0ddengr
  5

• Run against Eukrprot database did not complete successfully and Eukprot update request

  #66 opened 2 months ago by mkarlik93
  0

• Suppress opening of matplotlib figure opening

  #64 opened 3 months ago by paulzierep
  1

• buscu 5.6.1

  #62 opened 7 months ago by saky7009
  1

• Combining multiple samples

  #61 opened 7 months ago by susheelbhanu
  0

• --use_salmon_counts flag expects an argument on the command line

  #8 opened 9 months ago by cnatalie
  3

• some runs fail when downloading gtdb and marmmetsp

  #58 opened 9 months ago by danilodileo
  5

• Visualisation error

  #55 opened a year ago by susheelbhanu
  6

• Documentation update

  #54 opened 10 months ago by susheelbhanu
  2

• Print db version

  #57 opened a year ago by danilodileo
  1

• Taxonomy estimation step fails with eukprot

  #51 opened 2 years ago by cnatalie
  3

• Diamond did not complete successfully with rc code 1 Alignment did not complete successfully

  #56 opened a year ago by shanexuuu
  1

• Using multiple databases in the same run

  #53 opened a year ago by susheelbhanu
  2

• diamond --threads

  #50 opened 2 years ago by alephreish
  3

• Busco issue

  #49 opened 2 years ago by qfaber
  8

• Can you give EUKulele a custom diamond database? (e.g. RefSeq nr)

  #38 opened 2 years ago by jolespin
  4

• Setting customized evalue for filter_metric

  #48 opened 2 years ago by lsjmouse
  1

• Fail to install with Conda

  #47 opened 2 years ago by ZongzhiWu
  6

• Uninformative error when given empty fasta file

  #39 opened 2 years ago by jlw-ecoevo
  3

• Question: metagenomes or MAGs?

  #30 opened 2 years ago by Ahmed-Shibl
  1

• EUKulele Fails on "Performing taxonomic visualization steps..."

  #41 opened 3 years ago by tuck82er
  7

• Make DBs download in `--reference_dir`

  #10 opened 2 years ago by akrinos
  0

• Add Marzoanmmetsp database to next release

  #32 opened 2 years ago by halexand
  0

• Issues running EUKulele with .fnn file

  #37 opened 2 years ago by sgleich
  1

• EUKulele not recognizing downloaded db?

  #46 opened 2 years ago by nvpatin
  15

• Update documentation with default nucleotide extension

  #45 opened 2 years ago by cnatalie
  1

• EUKulele is making a Diamond database even though it already exists

  #44 opened 3 years ago by jolespin
  5

• How can I run with existing database?

  #43 opened 3 years ago by jolespin
  1

• Missing taxonomy_counts/test_all_division_counts.csv

  #36 opened 3 years ago by michoug
  7

• BUSCO error

  #14 opened 4 years ago by shu251
  11

• Question: Threads and estimated runtime

  #33 opened 4 years ago by susheelbhanu
  3

• Fasta output for those classified as euks

  #35 opened 4 years ago by susheelbhanu
  0

• Conda installation issue

  #34 opened 4 years ago by susheelbhanu
  5

• EUKulele setup database

  #31 opened 4 years ago by slaperriere
  4

• log database info within folder where run

  #28 opened 4 years ago by halexand
  1

• Conda installation fails

  #24 opened 4 years ago by johanneswerner
  8

• Clean up miscelaneous files that are written out

  #27 opened 4 years ago by halexand
  0

• Question on use with MAGs

  #23 opened 4 years ago by AstrobioMike
  2

• Think about changing output organization

  #15 opened 4 years ago by akrinos
  0

• Check if protein or nt before running alignment?

  #13 opened 4 years ago by halexand
  3

• Add EukZoo

  #9 opened 4 years ago by akrinos
  0

• Change log directory to be inside output directory

  #11 opened 4 years ago by akrinos
  0

• Make it so that just download happens with "download" subroutine

  #12 opened 4 years ago by akrinos
  1

• Allow the addition of one additional genome or transcriptome?

  #7 opened 4 years ago by halexand
  1

• Organizational pushes

  #4 opened 4 years ago by akrinos
  0