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

Morgan, Martin Martin.Morgan at roswellpark.org
Mon Nov 9 17:15:22 CET 2015

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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