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28 Open 8 Closed
28 Open 8 Closed
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Issues list

enable DOI citation of specific GBIF data
#82 opened Jul 27, 2023 by dnoesgaard
3 tasks
1
number of sequences does not match the number of individuals in the occurrence file
#78 opened Jun 24, 2022 by johrstrom
user flags
#77 opened Jun 23, 2022 by shastara
update GBIF and rerun with new accessions
#76 opened Jun 23, 2022 by shastara
sequence ID that doesn't follow system
#75 opened Jun 23, 2022 by shastara
copying duplicates in final alignment
#74 opened Jun 23, 2022 by shastara
full download error
#73 opened Jun 17, 2022 by shastara
2
parallelize link_gbif_with_genbank
#71 opened May 20, 2022 by johrstrom
GenBank and GBIF mismatch
#69 opened Apr 19, 2022 by johrstrom
1
Poor quality sequences not dropped
#63 opened Mar 12, 2022 by skdecker
1
majority of bold records are being filtered pipeline
#53 opened Feb 24, 2022 by johrstrom
new flag for manually updated records
#50 opened Feb 18, 2022 by johrstrom
mv genes.rb to pipeline pipeline
#31 opened Nov 19, 2021 by johrstrom
use csv library
#29 opened Nov 18, 2021 by johrstrom
gbif data filtered
#27 opened Nov 17, 2021 by johrstrom
2
speed up genbank download pipeline
#25 opened Nov 12, 2021 by johrstrom
Address species that have too long filenames because of accidentally using the long gene name form
#21 opened Nov 8, 2021 by johrstrom
2
After running pipeline, Cuculus-micropterus has no occurrences
#20 opened Nov 8, 2021 by johrstrom
1
Use a spacial index to speed up the queries
#19 opened Nov 8, 2021 by johrstrom
Speed up taxonomy table load
#18 opened Nov 8, 2021 by johrstrom
Expand bin/rake metrics:species to include detailed report statistics
#17 opened Nov 8, 2021 by johrstrom
Investigate using parallel_tests to execute rake tasks in parallel
#16 opened Nov 8, 2021 by johrstrom
different_genbank_species column in a genes index file doesn't capture all the variations
#15 opened Nov 8, 2021 by johrstrom
If a job submission fails, you get an error page
#14 opened Nov 8, 2021 by johrstrom
1
Drop MySQL dependency (so no centralized db server)
#13 opened Nov 8, 2021 by johrstrom
ProTip! Exclude everything labeled bug with -label:bug.