Looks like that was the issue, thanks Vincent & Martin! > hub = AnnotationHub() snapshotDate(): 2018-08-20 > isDevel() [1] TRUE
> query(hub, "Mus_musculus.GRCm38.93.chr.gtf") AnnotationHub with 1 record # snapshotDate(): 2018-08-20 # names(): AH63797 # $dataprovider: Ensembl # $species: Mus musculus # $rdataclass: GRanges # $rdatadateadded: 2018-07-31 # $title: Mus_musculus.GRCm38.93.chr.gtf # $description: Gene Annotation for Mus musculus # $taxonomyid: 10090 # $genome: GRCm38 # $sourcetype: GTF # $sourceurl: ftp://ftp.ensembl.org/pub/release-93/gtf/mus_musculus/Mus... # $sourcesize: 29183870 # $tags: c("GTF", "ensembl", "Gene", "Transcript", "Annotation") # retrieve record with 'object[["AH63797"]]' On Wed, Sep 26, 2018 at 2:01 PM Martin Morgan <mtmorgan.b...@gmail.com> wrote: > maybe you are not using the 'devel' version of Bioconductor? > > On 09/26/2018 03:48 PM, Bohdan Khomtchouk wrote: > > Martin, I don't see it unfortunately: > > > > > query(hub, "Mus_musculus.GRCm38.93.chr.gtf") > > AnnotationHub with 0 records > > # snapshotDate(): 2018-04-30 > > > > But perhaps it needs to be added to AnnotationHub, because I see other > > .chr.gtf files that go up to 86 (while I'm using 93 in this original > post): > > > > > query(hub, c("GTF", "Mus musculus", ".chr.gtf")) > > AnnotationHub with 112 records > > # snapshotDate(): 2018-04-30 > > # $dataprovider: Ensembl > > # $species: Mus musculus > > # $rdataclass: GRanges > > # additional mcols(): taxonomyid, genome, description, > > # coordinate_1_based, maintainer, rdatadateadded, preparerclass, > > # tags, rdatapath, sourceurl, sourcetype > > # retrieve records with, e.g., 'object[["AH50868"]]' > > > > title > > AH50868 | Mus_musculus.GRCm38.84.chr.gtf > > AH51038 | Mus_musculus.GRCm38.85.chr.gtf > > AH51979 | Mus_musculus.GRCm38.86.chr.gtf > > AH51983 | Mus_musculus_129s1svimj.129S1_SvImJ_v1.86.chr.gtf > > AH51986 | Mus_musculus_aj.A_J_v1.86.chr.gtf > > ... ... > > AH61202 | Mus_musculus_lpj.LP_J_v1.92.chr.gtf > > AH61205 | Mus_musculus_nodshiltj.NOD_ShiLtJ_v1.92.chr.gtf > > AH61208 | Mus_musculus_nzohlltj.NZO_HlLtJ_v1.92.chr.gtf > > AH61211 | Mus_musculus_pwkphj.PWK_PhJ_v1.92.chr.gtf > > AH61214 | Mus_musculus_wsbeij.WSB_EiJ_v1.92.chr.gtf > > > > So it looks like "AH51979 | Mus_musculus.GRCm38.86.chr.gtf" is the > > latest one available in AnnotationHub right now. > > > > > > On Tue, Sep 25, 2018 at 10:35 PM Martin Morgan <mtmorgan.b...@gmail.com > > <mailto:mtmorgan.b...@gmail.com>> wrote: > > > > Good news, the file is in AnnotationHub and can be used from there. > > There is a download cost the first time but not subsequently. > > > > library(AnnotationHub) > > hub = AnnotationHub() > > query(hub, "Mus_musculus.GRCm38.93.chr.gtf.gz") > > > > ## note 'AH' number, then... > > gtf = hub[["AH63797"]] > > > > Need the path rather than the imported path? use > cache(hub["AH63797"]) > > instead. > > > > Martin > > > > On 09/25/2018 09:59 PM, Bohdan Khomtchouk wrote: > > > To generate mouse.rda, I used: > > > > > > library(rtracklayer) > > > mouse <- readGFF(" > > > > > > ftp://ftp.ensembl.org/pub/release-93/gtf/mus_musculus/Mus_musculus.GRCm38.93.chr.gtf.gz > > > ") > > > > > > And then I saved the object as mouse.rda > > > > > > > > > On Tue, Sep 25, 2018 at 6:33 PM Bohdan Khomtchouk > > <khomtchouk...@gmail.com <mailto:khomtchouk...@gmail.com>> > > > wrote: > > > > > >> Here it is: > > >> > > > https://github.com/Bohdan-Khomtchouk/geneXtendeR/blob/master/data/mouse.rda > > >> > > >> > > >> On Tue, Sep 25, 2018 at 6:23 PM Vincent Carey > > <st...@channing.harvard.edu <mailto:st...@channing.harvard.edu>> > > >> wrote: > > >> > > >>> (resending with reply all -- please reply to this one) > > >>> > > >>> Can you say some more about the content of the file? Perhaps > > it can be > > >>> placed in ExperimentHub. "mouse.rda" is not very descriptive. > > is it > > >>> in your github repo? > > >>> > > >>> > > >>> On Tue, Sep 25, 2018 at 6:25 PM, Bohdan Khomtchouk < > > >>> khomtchouk...@gmail.com <mailto:khomtchouk...@gmail.com>> > wrote: > > >>> > > >>>> I need to include an important .rda file in the /data folder > of my > > >>>> Bioconductor package. However, this .rda file exceeds 5 Mb in > > size. Do > > >>>> I > > >>>> have any other options besides for deleting it? > > >>>> > > >>>> bohdankhomtchouk$ git push origin master > > >>>> > > >>>> Counting objects: 65, done. > > >>>> > > >>>> Delta compression using up to 8 threads. > > >>>> > > >>>> Compressing objects: 100% (65/65), done. > > >>>> > > >>>> Writing objects: 100% (65/65), 13.79 MiB | 7.62 MiB/s, done. > > >>>> > > >>>> Total 65 (delta 30), reused 0 (delta 0) > > >>>> > > >>>> remote: Error: file larger than 5 Mb. > > >>>> > > >>>> remote: > > >>>> > > >>>> remote: File name: 'data/mouse.rda' > > >>>> > > >>>> remote: File size: 12.9 Mb > > >>>> > > >>>> remote: > > >>>> > > >>>> remote: Please see Biocondcutor guidelines > > >>>> > > >>>> remote: > https://bioconductor.org/developers/package-guidelines/ > > >>>> > > >>>> remote: > > >>>> > > >>>> To git.bioconductor.org:packages/geneXtendeR > > >>>> > > >>>> ! [remote rejected] master -> master (pre-receive hook > declined) > > >>>> > > >>>> error: failed to push some refs to 'g...@git.bioconductor.org > > <mailto:g...@git.bioconductor.org>: > > >>>> packages/geneXtendeR' > > >>>> > > >>>> -- > > >>>> Bohdan Khomtchouk, Ph.D. > > >>>> AHA Postdoctoral Fellow, Gozani & Assimes Labs > > >>>> Department of Biology & Department of Medicine > > >>>> Division of Cardiovascular Medicine > > >>>> Stanford University > > >>>> Stanford, CA 94305 > > >>>> https://profiles.stanford.edu/bohdan-khomtchouk > > >>>> > > >>>> > > >>>> CONFIDENTIALITY NOTICE: Information contained in this > > me...{{dropped:9}} > > >>>> > > >>>> _______________________________________________ > > >>>> Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> > > mailing list > > >>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel > > >>>> > > >>> > > >>> > > >>> The information in this e-mail is intended only for > > t...{{dropped:17}} > > > > > > _______________________________________________ > > > Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> > > mailing list > > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > > > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
