Add SNPchip as a dependency.

[roryk]

Luca brought this up here bcbio/bcbio-nextgen#2874, the dependency is checked for here, but isn't included in the DESCRIPTION as a dependency. This adds it.

Thanks!

If this pull request is mangled, forgive me, trying out hub for the first time. :)

[gavinha]

Hi @roryk

Thank you for bringing up this issue and carrying the discussion in https://github.com/bcbio/bcbio-nextgen/issues/2874. While SNPchip is currently being used to plot the idiogram, it is not actually necessary within the TitanCNA R package itself. It is being used in the titanCNA.R script, which is provided as a convenience for the user to run TITAN without having build this script themselves. That is, it is the series of commands from the vignette.

Thanks, Gavin

[roryk]

Hi Gavinha,

Doesn't that mean it is a dependency? This means that TitanCNA is shipping with a script that doesn't work unless you install SNPchip yourself. Since it isn't added as a dependency, it doesn't get picked up by any of the automated builds that bioconductor or bioconda does, so it is shipping with a broken script. Could you reconsider adding this as a dependency?

[gavinha]

Hi @roryk

Thanks for your comment. I am in the process of moving the snakemake workflow out of the TitanCNA repo. And so the titanCNA.R script will also leave with it. Then, I'll be removing the SNPchip requirement in the vignette if it's not already removed.

My thinking is this TitanCNA repo should stay as just the R package only while workflows can be separate. I've found that most of the minor tinkering and PRs are usually related to the snakemake worflow and the titanCNA.R script.

[roryk]

Gotcha-- thanks for the clarification, I definitely understand trying to manage support overhead.