your annotation hub is out of date. run hub = AnnotationHub() and try again
On Wed, Sep 26, 2018 at 3:48 PM, Bohdan Khomtchouk <khomtchouk...@gmail.com> 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> > 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> >> > 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> >> >> 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> 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: >> >>>> 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 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 mailing list >> > https://stat.ethz.ch/mailman/listinfo/bioc-devel >> > >> > -- The information in this e-mail is intended only for the ...{{dropped:18}} _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel