standage/genhub

Issues

• Extend RefSeq module with support for GenBank

  #36 opened 7 years ago by standage
  0

• Checksums missing for G. raimondii config

  #76 opened 8 years ago by standage
  1

• Easily identify piLocus representatives

  #81 opened 8 years ago by standage
  1

• Create spec file for GFF3 input, integrate into workflow

  #80 opened 8 years ago by standage
  0

• nose --> py.test

  #73 opened 8 years ago by standage
  0

• New Amel genome

  #75 opened 8 years ago by standage
  0

• Option for overriding integrity (shasum) check

  #74 opened 8 years ago by standage
  1

• .txt --> .tsv for some ancillary data files

  #71 opened 8 years ago by standage
  2

• Add documentation for creating new .yml config files

  #72 opened 8 years ago by standage
  0

• Configuration registry is cumbersome

  #60 opened 9 years ago by standage
  0

• Support for generic input

  #66 opened 9 years ago by standage
  1

• Deprecate `*.simple-iloci.txt` file

  #69 opened 9 years ago by standage
  1

• piLocus type for pre-mRNA, mRNA, exon, and intron TSV files

  #67 opened 9 years ago by standage
  0

• More species to integrate

  #7 opened 9 years ago by standage
  1

• Allow user to override cd-hit defaults

  #51 opened 9 years ago by standage
  0

• New rice recipe?

  #49 opened 9 years ago by standage
  0

• NT_ and NW_ accessions in mammalian genomes correspond to patches, variants

  #52 opened 9 years ago by standage
  0

• Add `delta` option to genhub-build script

  #48 opened 9 years ago by standage
  0

• Overlapping exons prematurely kill C. reinhardtii build

  #47 opened 9 years ago by standage
  0

• Better handling of multiprocessing pool

  #40 opened 9 years ago by standage
  0

• Recipes for green algae

  #41 opened 9 years ago by standage
  0

• Recipes for specific versions

  #39 opened 9 years ago by standage
  2

• Test whether ilens file can be ignored

  #35 opened 9 years ago by standage
  0

• Polish documentation, dev environment

  #28 opened 9 years ago by standage
  1

• Switch over to newer NCBI genomes FTP

  #19 opened 9 years ago by standage
  1

• More PycURL stuff

  #30 opened 9 years ago by standage
  0

• Improve configuration parsing

  #15 opened 9 years ago by standage
  3

• Move, rename config files

  #29 opened 9 years ago by standage
  0

• Pass source to `genhub-format-gff3.py`

  #16 opened 9 years ago by standage
  0

• Refactor `format.py`

  #17 opened 9 years ago by standage
  0

• Dmel format task fails

  #13 opened 9 years ago by standage
  0

• Support for lists of conf files

  #6 opened 9 years ago by standage
  0

• Cache dependencies

  #5 opened 9 years ago by standage
  1

• Script paths during build

  #3 opened 9 years ago by standage
  0

• Script names

  #4 opened 9 years ago by standage
  0

• Consolidate file name resolution

  #2 opened 9 years ago by standage
  0

• Update `check.py` to check for PATH dependencies

  #1 opened 9 years ago by standage
  0