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hbc / bcbioRNASeq

R package for bcbio RNA-seq analysis.
https://bioinformatics.sph.harvard.edu/bcbioRNASeq
GNU Affero General Public License v3.0
58 stars 21 forks source link

bioconda package #130

Closed roryk closed 5 years ago

roryk commented 5 years ago

Hey @mjsteinbaugh,

There is a new bioconda bot which pushes new releases automatically when it spies new releases, unfortunately this means the bioconda recipe for bcbioRNASeq is broken since it won't have all of the new dependencies, as they are not in bioconda and aren't listed in the bcbioRNASeq recipe. I think these two are missing:

    DESeqAnalysis (>= 0.2.0)
    acidplots (>= 0.2.7)
roryk commented 5 years ago

https://github.com/bioconda/bioconda-recipes/blob/master/recipes/r-bcbiornaseq/meta.yaml has the current dependency list.

   - r-base
    - bioconductor-summarizedexperiment
    - r-bcbiobase
    - bioconductor-deseq2
    - bioconductor-degreport
    - bioconductor-edger
    - r-ggrepel
    - r-pbapply
    - bioconductor-tximport
    - bioconductor-vsn
    - r-rmarkdown
    - r-tidyverse
    - bioconductor-genomeinfodbdata
    - r-hexbin

looks like it is also missing the bioverbs dependency.

mjsteinbaugh commented 5 years ago

@roryk I’m working on updating the recipes today

roryk commented 5 years ago

Thanks!

mjsteinbaugh commented 5 years ago

bioconda update is in progress.