[Bioc-devel] Dependency files question

[Shepherd, Lori]

We would probably recommended having an associated data package that utilizes ExperimentHub.  Please see
 http://bioconductor.org/packages/release/bioc/vignettes/ExperimentHub/inst/doc/CreateAnExperimentHubPackage.html

Please let me know if you have any follow up questions.

Cheers


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Alexandru Voda <alexandru.voda using seh.ox.ac.uk>
Sent: Monday, March 2, 2020 6:51 AM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: [Bioc-devel] Dependency files question

Hi!

Hope this finds you well!

I was told to contact this mailing list about preparing/changing a package for Bioconductor submission.

My question is: How should I store large dependency files - 6GB large (e.g. 1000 genomes reference LD data) - for the package on Bioconductor?

My package wraps multiple methods of cell-typing GWAS summary statistics. The problem is that the methods wrapped by my package require dependency files for analyses to run, and those dependency files are very large. In my github package, I simply made a function that downloads and formats all of the data in the package's system path, in the data folder: paste0(system.file(package="GWASCellTyper"), "/data/")

Link to the package in its current state: https://bitbucket.org/alexandru_ioan_voda/cell_typing_package/src/master/


With best wishes,

Alexandru Ioan Voda

        [[alternative HTML version deleted]]

_______________________________________________
Bioc-devel using r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel


This email message may contain legally privileged and/or confidential information.  If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited.  If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
	[[alternative HTML version deleted]]