WrightonLabCSU/DRAM

Issues

• State of DRAM2

  #361 opened 2 months ago by donovan-parks
  1

• Controlling CPU usage for the DRAM.py distill pipeline for DRAM v.1.5.0

  #358 opened 3 months ago by nataliesarno
  1

• Add much better logging throughout the pipeline

  #382 opened a month ago by madeline-scyphers
  0

• Add better input validation for input combinations that don't make sense

  #381 opened a month ago by madeline-scyphers
  0

• Dram-v on Virsorter2 output: pandas error, unexpected EOF, syntax error

  #363 opened a month ago by deminatanja
  1

• Create a DOI for the DRAM software with zenodo

  #380 opened a month ago by madeline-scyphers
  0

• Add testing suite for Nextflow and add back DRAM v1 testing suite for v2

  #368 opened a month ago by madeline-scyphers
  0

• `input_fasta` argument has to end with `/` otherwise `fasta_fmt` doesn't get appended properly

  #379 opened a month ago by madeline-scyphers
  0

• Better user Nextflow Configuration override

  #371 opened a month ago by madeline-scyphers
  0

• Update docs from Wiki for DRAM v2, probably move to readthedocs

  #367 opened a month ago by madeline-scyphers
  0

• When writing outputs or logs, if already exists, append with something

  #378 opened a month ago by madeline-scyphers
  0

• All CLI help text defaults should pull from the config default, the config defualt instead of being hard coded

  #377 opened a month ago by madeline-scyphers
  0

• Add close inactive issue workflow/action

  #376 opened a month ago by madeline-scyphers
  0

• Setup milestones for tracking issues and development progress

  #375 opened a month ago by madeline-scyphers
  0

• DRAM visualization (product) tracking issue

  #374 opened a month ago by madeline-scyphers
  0

• DRAM v2 README has too much hard coded things in it (like the --help output)

  #373 opened a month ago by madeline-scyphers
  0

• DRAM trees and adjectives implementation

  #372 opened a month ago by madeline-scyphers
  0

• Update environment.yml

  #370 opened a month ago by madeline-scyphers
  0

• Integrate whatever we feel is useful from the nf-core template

  #369 opened a month ago by madeline-scyphers
  1

• Decouple DRAM v2 tool code from Nextflow code

  #366 opened a month ago by madeline-scyphers
  0

• KEGG db formatting process should allow passing in directory of pep files

  #365 opened a month ago by madeline-scyphers
  0

• set_database_locations results in TypeError: DatabaseHandler.set_database_paths() got an unexpected keyword argument 'camper_tar_gz_loc'

  #355 opened 4 months ago by jehalter0
  1

• ListUtil.c: loadable library and perl binaries are mismatched

  #362 opened 2 months ago by 473021677
  0

• DRAM database installation problem; The subcommand mmseqs createindex DRAM_data/uniref90.20240308.mmsdb DRAM_data/tmp --threads 10 experienced an error

  #336 opened 8 months ago by camillaln
  4

• DRAM-setup.py in v1.5.0 has invalid syntax

  #360 opened 2 months ago by donovan-parks
  0

• ValueError: Format is not VIRSorter2, and can't find VIRSorter endings on fasta header

  #359 opened 2 months ago by liaohu1231
  4

• errors when prepare database

  #349 opened 6 months ago by mengyuan-JI
  4

• Fix `DRAM-setup.py` v1.5.0 for missing `)`

  #339 opened 8 months ago by npavlovikj
  5

• Pathway abundances?

  #357 opened 3 months ago by Manso002
  0

• Changing order of genomes in DRAM distill HTML output

  #356 opened 4 months ago by iwilkie
  1

• pop out errors when prepare databases

  #354 opened 4 months ago by lingc31415
  0

• VOGDB does not import correctly

  #353 opened 5 months ago by nactopus
  1

• distill: AttributeError: 'list' object has no attribute 'concat'

  #351 opened 5 months ago by marina-vn
  0

• Fail in processing vogdb

  #341 opened 8 months ago by ShangLiii
  6

• Selection logic for gene_id in amg_summery.tsv

  #350 opened 5 months ago by diego00012138
  1

• bug in `v.1.5.0` on the `DRAM-setup.py` help message

  #334 opened 9 months ago by hariszaf
  1

• `genome_stats.tsv` has the wrong tRNA count for MIMAG standards

  #348 opened 6 months ago by AroneyS
  3

• Problem with database instalation (vog_latest_hmms.txt is empty)

  #342 opened 7 months ago
  2

• How long does populating step take?

  #345 opened 7 months ago by jianshu93
  3

• DRAM2 environment.yaml

  #346 opened 6 months ago by SF-Dragon
  1

• DRAM 1.5.0 installation issues

  #330 opened 10 months ago by karenhn
  6

• problem about dramv-annotate

  #335 opened 8 months ago by xjhzjucas
  3

• hmmpress not found during prepare_databases

  #332 opened 9 months ago by carleton-envbiotech
  1

• AttributeError: 'Series' object has no attribute 'iteritems'

  #347 opened 6 months ago by sahilrishav2
  0

• Need help in processing of database

  #343 opened 6 months ago by sahilrishav2
  0

• Need help in preparation of database

  #344 opened 6 months ago by sahilrishav2
  0

• Continue the "prepare_database" process

  #333 opened 9 months ago by chenyj8
  2

• VOGDB issue--extra enclosing folder

  #340 opened 8 months ago by schmigle
  4

• cazy annotation format for version 1.4.6

  #338 opened 8 months ago by Ales-ibt
  1

• dbcan2 url gone ??

  #331 opened 9 months ago by EricDeveaud
  3