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oncogenetics / LocusExplorer

An interactive graphical illustration of genetic associations and their biological context
MIT License
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Example input data: Please download Histone bigWig files #39

Closed AngieHinrichs closed 9 years ago

AngieHinrichs commented 9 years ago

When I use the Example data in Plot Settings, and check all of the tracks, I can see data for all of them except for Histone - instead of data it has the message:

Please download Histone bigWig files!

And I don't see anything about how to incorporate those in the Help tabs.

zx8754 commented 9 years ago

Hi @AngieHinrichs

I added FAQ panel in Help tab.

You can see the FAQ.md markdown file here, see question number 5.

Thanks Tokhir

AngieHinrichs commented 9 years ago

Great to see the FAQ. Yes, the bigWig files are quite large so I can see why you wouldn't want to redistribute them via github!

I can't tell where runGitHub (http://www.inside-r.org/packages/cran/shiny/docs/runGitHub) puts the local files -- seems not to be in the directory where I'm running R, nor in /tmp -- ha, it appears to be $TMPDIR/Rtmpzghwdp/shinyapp13e24f209da5/LocusExplorer-master/Data/wgEncodeBroadHistone/. (Note: wgEncodeBroadHistone not EncodeBigWig as in the FAQ) Good luck to less persistent github/R n00bs. :) Anyway, no rush, but it would be nice to have a note in LocusExplorer/README.md (section Launch Locus Explorer) and/or the FAQ about how to download and run it without runGitHub in order to install the files locally. (The convenience of runGitHub is great for getting started, though!)

AngieHinrichs commented 9 years ago

[FWIW Seems it can't be shoehorned into runGitHub's tmp dir anyway -- it looks like the server needs to see the files when it starts up, but if I runGitHub() again then it will re-download the tar file and make a new tmp dir. No big deal, LocusExplorer and the files should be installed properly anyway.]

zx8754 commented 9 years ago

@AngieHinrichs OK, I will add Download as ZIP option, so the user knows the location of files, and can add bigwig into right folder. runGitHub() is a quick one, but with limitations, I shall make a note about this in the main README file.