Hi guys, OTOH indexMTGenome() only takes 20s on my laptop to create, install and load GmapGenome.Hsapiens.rCRS.
Note that the size on disk of GmapGenome.Hsapiens.rCRS is 449M which is surprising considering that the input of indexMTGenome() is a tiny 83K FASTA file. That's for the source tree. 'R CMD build' then produces a source tarball that is only 24M so is much reduced. Seems like the big files in GmapGenome.Hsapiens.rCRS are very sparse! Anyway this seems to be a reference genome so maybe would best belong to AnnotationHub? Cheers, H. On 11/9/18 08:42, Obenchain, Valerie wrote: > Hi Tim, > > The options would be to make a data experiment package or put the data > in ExperimentHub. > > Lori is our resident expert on these things but is out today. She'll be > back next week and can provide more info. > > Valerie > > > On 11/8/18 9:27 AM, Tim Triche, Jr. wrote: >> What's the best/fastest way to do this? The package (MTseeker) will happily >> build and install it for the user via the indexMTgenome() function, but >> since I test for its presence prior to running examples, it seems like I >> might as well have it available through BioC. >> >> Thanks, >> >> --t >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIFAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=CJuHqYXh0XkBMrSjP3aaWmkdZALDlc5ycy4MRQVDkEc&s=OCFa2kt3VaWZzfqcvZGzIQr-61UL0B2ibC7J2EhbPfc&e= >> > > > 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. > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIFAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=CJuHqYXh0XkBMrSjP3aaWmkdZALDlc5ycy4MRQVDkEc&s=OCFa2kt3VaWZzfqcvZGzIQr-61UL0B2ibC7J2EhbPfc&e= -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
