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119 Open 44 Closed
119 Open 44 Closed
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Issues list

Does charcoal not support installation via mamba?
#238 opened Oct 19, 2023 by SchwarzEM
16
Both DEMO datasets Fails with: ImportError: cannot import name 'LineagePair' from 'sourmash.lca'
#237 opened Jul 3, 2023 by JoshuaTCooper
1
1
Error in rule combine_postprocessing_csv
#236 opened Mar 7, 2023 by sabdelrazek
GenBank genomes not found
#235 opened Feb 16, 2023 by tgurbich
2
demo fails with "Error in snakemake invocation: Command '['snakemake', '-s', '/home/hh.nku.edu/cooperjo/software/charcoal/charcoal/Snakefile', '--use-conda', '-j', '1', '-j', '4', '--configfile', '/home/hh.nku.edu/cooperjo/software/charcoal/charcoal/conf/defaults.conf', '/home/hh.nku.edu/cooperjo/software/charcoal/charcoal/conf/system.conf', 'demo/demo.conf']' returned non-zero exit status 1."
#233 opened Feb 10, 2023 by JoshuaTCooper
What should we benchmark?
#232 opened Dec 20, 2022 by ccbaumler
3
paper: Contamination detection and microbiome exploration with GRIMER
#231 opened Dec 15, 2022 by ctb
explore unicity distance of individual contigs in database
#230 opened Nov 23, 2022 by ctb
charcoal analysis of single assembly file
#229 opened Oct 20, 2022 by gaworj
3
update database download to farm links
#228 opened Sep 5, 2022 by ctb
add test requirements to ...environment? pip install? something?
#227 opened Aug 24, 2022 by ctb
1
update env-reporting.yml version pins
#226 opened Aug 23, 2022 by ctb
3
demo fails with "Error occurred while starting new kernel client for kernel 0287ef32-45b2-4f5d-8470-97ab4a40626a: Kernel didn't respond in 60 seconds"
#222 opened Jul 13, 2022 by taylorreiter
5
add a disclaimer to the quickstart that it will take longer than 2min if the envs need to be created (e.g. first time running)?
#221 opened Jul 13, 2022 by taylorreiter
change quick start installation to mamba?
#220 opened Jul 13, 2022 by taylorreiter
Add tests for system conf scaled and gather_scaled values to match the default database scaled? testing
#219 opened Jun 23, 2022 by taylorreiter
add developer docs documentation Improvements or additions to documentation
#216 opened Jun 17, 2022 by taylorreiter
allow gzipped lineage files
#214 opened Jun 1, 2022 by taylorreiter
DEMO FAILED
#213 opened May 10, 2022 by giriarteS
config parameterization of GATHER_MIN_MATCHES enhancement New feature or request
#211 opened Mar 9, 2022 by taylorreiter
I think provided_lineages_file is no longer optional
#210 opened Mar 1, 2022 by taylorreiter
R parsers for stage1 and stage2 json files
#209 opened Feb 23, 2022 by taylorreiter
1
organization of report directory
#208 opened Feb 21, 2022 by taylorreiter
confused about some text in output of stage2 stage2/*postprocess.txt
#207 opened Feb 21, 2022 by taylorreiter
output stage1_genome_summary.csv during target clean enhancement New feature or request outputs
#206 opened Feb 18, 2022 by taylorreiter
3
ProTip! Exclude everything labeled bug with -label:bug.