[Bioc-devel] Pipeline management (and AnnotationData Packages version)

Elena Grassi grassi.e at gmail.com
Mon Jun 20 11:49:21 CEST 2016

On Mon, Jun 20, 2016 at 11:36 AM, Sean Davis <seandavi at gmail.com> wrote:
> Hi, Elena.
> What do your pipelines need to do?

The idea behind our system is to be as general as possible. We are
mainly interested in human genomic/transcriptomic...we stem from
standard differential expression analyses
on microarray/RNAseq data to support wet biologists to eQTL analyses and so on.

> In what environment do they run (cluster, single machine, lots of big data, or smallish data)?

Right now we are working with a single machine but the system is able
(and in the past we used it in this way) to submit jobs to a PBS.
Data: I would say that even in this case there is no general rule :/

> What are your priorities for the management system (language, reproducibility, flexibility, publication, sharing)?

Language flexibility is certainly the main issue along with reproducibility.

$ pom

More information about the Bioc-devel mailing list