Update SICER to include more genome builds (ideally all on the instance)

galaxyproject / tools-devteam

Contains a set of Galaxy Tools mostly written by the Galaxy Team.

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Update SICER to include more genome builds (ideally all on the instance) #390

Open jennaj opened 8 years ago

jennaj commented 8 years ago

The list of builds is outdated. At a minimum add the latest builds from the same organisms already included: mm10, hg38, dm6, sacCer3, rn5, rn6.

The "pombe" and "tair8" are not dbkeys in current Galaxy releases ... (??) but there are alternatives.

Quote from sicer_wrapper.py

HACK! FIXME: allow using all specified builds, would currently require hacking SICER's "GenomeData.py" on the fly.

VALID_BUILDS = [ 'mm8', 'mm9', 'hg18', 'hg19', 'dm2', 'dm3', 'sacCer1', 'pombe', 'rn4', 'tair8' ]

ACastanza commented 7 years ago

I'd also like to see this updated, seems a little weird that so many of these tools (and related publications) are still using mm9.

jennaj commented 6 years ago

ping @martenson @davebx @nekrut

Are there plans to update this tool? Was asked about again here: https://biostar.usegalaxy.org/p/28442/. Thanks!