[Bioc-devel] Gviz: implementing support for FaFiles from AnnotationHub

Rainer Johannes Johannes.Rainer at eurac.edu
Mon Nov 9 19:52:56 CET 2015

thanks Martin,

I will consider that… although I did already lots of changes, so I have to figure out how to do that.
Actually, I start appreciating the "pull request” approach from github… working simultaneously with git and svn can be quite tricky.

cheers, jo

> On 09 Nov 2015, at 17:15, Morgan, Martin <Martin.Morgan at roswellpark.org> wrote:
> For what it's worth and from an earlier comment in this thread, one way to use git (for Johanne's benefit) within the context of svn (for Florian's benefit) is to svn co Gviz, then on top of svn create a new git repository branch and update at will, then merge changes to master and provide florian with svn diff. Something like
>    svn co https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Gviz
>    cd Gviz/
>    git init 
>    git add .
>    git commit -a -m "initial commit"
>    git checkout -b my_mods
>    ## amazing changes
>    git commit -a -m "my amazing changes"
>    git checkout master 
>    svn st                        # no changes
>    git merge my_mods 
>    svn st                         # my amazing changes
>    svn diff > Gviz.diff     # ... as a diff for Florian
> ________________________________________
> From: Bioc-devel [bioc-devel-bounces at r-project.org] on behalf of Rainer Johannes [Johannes.Rainer at eurac.edu]
> Sent: Monday, November 09, 2015 10:08 AM
> To: bioc-devel at r-project.org
> Subject: [Bioc-devel] Gviz: implementing support for FaFiles from       AnnotationHub
> Dear All, dear Florian,
> I’m currently working on a Gviz-hack that would enable to use the FaFiles provided from AnnotationHub directly as SequenceTracks in Gviz. I think that might be a nice addition, since that way both Ensembl based annotations (e.g. as EnsDbs) and Ensembl genome fasta files (provided by AnnotationHub) could be used.
> So, Florian, eventually I’m going to send you some more files.
> cheers, jo
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