Thanks! I will check it out.




Van: Ross []
Verzonden: donderdag 20 december 2012 9:52
Aan: Bossers, Alex
CC: Samuel Lampa;
Onderwerp: Re: [galaxy-dev] Integrating generated graphics from cli tool?


Alex, xvfb works for our headless node R graphics and possibly other packages.

I seem to remember writing a wiki entry but a search didn't find it...


I see someone on the dev list found the toolfactory code which does a lot of sensible things automatically to create a pretty useful html index for a folder full of pdfs/pngs/xls/....


On Mon, Dec 17, 2012 at 11:14 PM, Bossers, Alex <> wrote:

We do the same as Peter mentioned.
We generate pdfs or you could generate a mixed datatype html file linking to seperate documents/images (like the fastQC tool).
If you get the export to png working on a headless server without desktop/gui..please let me know. In our hands it only works on full desktop linux environments somehow.

-----Oorspronkelijk bericht-----
Van: [] Namens Samuel Lampa
Verzonden: zondag 16 december 2012 23:14
Aan: Peter Cock
Onderwerp: Re: [galaxy-dev] Integrating generated graphics from cli tool?

On 12/14/2012 07:40 PM, Peter Cock wrote:
> On Fri, Dec 14, 2012 at 6:18 PM, Samuel Lampa <> wrote:
> There are existing tools which produce a PDF file as a Galaxy output,
> shown as its own 'green box' in the history. This works quite nicely
> if the browser shows the PDF in-line, but one one of my machines (not
> sure which browser off hand) it insists on downloading the PDF and
> opening it instead - which isn't quite as smooth an interface.

Thanks for the info!

Seems like that could be one way of doing it. I would probably output png rather than pdf, and that might work better.

// Samuel