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}}
>
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