AlexanderLabWHOI/EUKulele issues and pull requests

#66 - Run against Eukrprot database did not complete successfully and Eukprot update request

Issue - State: open - Opened by mkarlik93 5 months ago - 1 comment

#65 - Improve DB download option

Issue - State: open - Opened by paulzierep 5 months ago - 2 comments

#64 - Suppress opening of matplotlib figure opening

Issue - State: open - Opened by paulzierep 6 months ago - 1 comment

#63 - Mamba install for eukulele=2.0.7 is problematic

Issue - State: closed - Opened by g0ddengr 9 months ago - 5 comments

#62 - buscu 5.6.1

Issue - State: closed - Opened by saky7009 9 months ago - 1 comment

#61 - Combining multiple samples

Issue - State: open - Opened by susheelbhanu 9 months ago - 2 comments

#60 - EUKulele v2.0.7 fails taxonomy estimation step

Issue - State: closed - Opened by danilodileo 11 months ago - 1 comment

#59 - No samples found in sample directory with specified peptide extension.

Issue - State: closed - Opened by shibormi 12 months ago - 6 comments

#58 - some runs fail when downloading gtdb and marmmetsp

Issue - State: open - Opened by danilodileo 12 months ago - 5 comments

#57 - Print db version

Issue - State: open - Opened by danilodileo about 1 year ago - 1 comment

#56 - Diamond did not complete successfully with rc code 1 Alignment did not complete successfully

Issue - State: closed - Opened by shanexuuu about 1 year ago - 1 comment

#55 - Visualisation error

Issue - State: open - Opened by susheelbhanu about 1 year ago - 6 comments

#54 - Documentation update

Issue - State: closed - Opened by susheelbhanu about 1 year ago - 2 comments

#53 - Using multiple databases in the same run

Issue - State: open - Opened by susheelbhanu about 1 year ago - 2 comments

#52 - Cant install from Mamba

Issue - State: closed - Opened by blsteven over 1 year ago - 5 comments

#51 - Taxonomy estimation step fails with eukprot

Issue - State: open - Opened by cnatalie over 1 year ago - 3 comments

#50 - diamond --threads

Issue - State: closed - Opened by alephreish almost 2 years ago - 4 comments

#49 - Busco issue

Issue - State: open - Opened by qfaber almost 2 years ago - 8 comments

#48 - Setting customized evalue for filter_metric

Issue - State: closed - Opened by lsjmouse about 2 years ago - 1 comment

#47 - Fail to install with Conda

Issue - State: open - Opened by ZongzhiWu over 2 years ago - 6 comments

#46 - EUKulele not recognizing downloaded db?

Issue - State: closed - Opened by nvpatin over 2 years ago - 15 comments

#45 - Update documentation with default nucleotide extension

Issue - State: closed - Opened by cnatalie over 2 years ago - 1 comment

#44 - EUKulele is making a Diamond database even though it already exists

Issue - State: open - Opened by jolespin over 2 years ago - 5 comments

#43 - How can I run with existing database?

Issue - State: closed - Opened by jolespin over 2 years ago - 1 comment

#42 - Providing added functionality to the LCA method & removing BUSCO dependency

Pull Request - State: closed - Opened by akrinos over 2 years ago

#41 - EUKulele Fails on "Performing taxonomic visualization steps..."

Issue - State: open - Opened by tuck82er almost 3 years ago - 7 comments

#40 - Visualization Error

Issue - State: closed - Opened by MichielPerneel about 3 years ago - 2 comments

#39 - Uninformative error when given empty fasta file

Issue - State: closed - Opened by jlw-ecoevo about 3 years ago - 3 comments

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

Issue - State: closed - Opened by jolespin over 3 years ago - 4 comments

#37 - Issues running EUKulele with .fnn file

Issue - State: closed - Opened by sgleich over 3 years ago - 1 comment

#36 - Missing taxonomy_counts/test_all_division_counts.csv

Issue - State: open - Opened by michoug over 3 years ago - 7 comments

#35 - Fasta output for those classified as euks

Issue - State: open - Opened by susheelbhanu over 3 years ago

#34 - Conda installation issue

Issue - State: closed - Opened by susheelbhanu almost 4 years ago - 5 comments

#33 - Question: Threads and estimated runtime

Issue - State: closed - Opened by susheelbhanu almost 4 years ago - 3 comments

#32 - Add Marzoanmmetsp database to next release

Issue - State: closed - Opened by halexand almost 4 years ago

#31 - EUKulele setup database

Issue - State: open - Opened by slaperriere almost 4 years ago - 4 comments

#30 - Question: metagenomes or MAGs?

Issue - State: closed - Opened by Ahmed-Shibl almost 4 years ago - 1 comment

#29 - Minor formatting fixes.

Pull Request - State: closed - Opened by arfon almost 4 years ago

#28 - log database info within folder where run

Issue - State: open - Opened by halexand almost 4 years ago - 1 comment

#27 - Clean up miscelaneous files that are written out

Issue - State: open - Opened by halexand about 4 years ago

#26 - fixed small typos

Pull Request - State: closed - Opened by johanneswerner about 4 years ago

#25 - fix installation commands in quickstart

Pull Request - State: closed - Opened by will-rowe about 4 years ago

#24 - Conda installation fails

Issue - State: closed - Opened by johanneswerner about 4 years ago - 8 comments