Integrating generated graphics from cli tool?
Hi, I'm looking into integrating some R scripts into Galaxy, which create some graphics / plots. We are interested in integrating those in galaxy somehow, or otherwise presenting them to the user in an as easy way as possible. I wanted to check if there is some support for this kind of functionality there already, or if I'll need to hack something together myself? (I couldn't really find anything here on the mailing list). Many TIA! Best // Samuel -- Developer at SNIC-UPPMAX www.uppmax.uu.se Developer at Dept of Pharm Biosciences www.farmbio.uu.se
On Fri, Dec 14, 2012 at 6:18 PM, Samuel Lampa <samuel.lampa@gmail.com> wrote:
Hi,
I'm looking into integrating some R scripts into Galaxy, which create some graphics / plots. We are interested in integrating those in galaxy somehow, or otherwise presenting them to the user in an as easy way as possible.
I wanted to check if there is some support for this kind of functionality there already, or if I'll need to hack something together myself?
(I couldn't really find anything here on the mailing list).
Many TIA!
Best // Samuel
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. Peter
On 12/14/2012 07:40 PM, Peter Cock wrote:
On Fri, Dec 14, 2012 at 6:18 PM, Samuel Lampa <samuel.lampa@gmail.com> 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. Best // Samuel -- Developer at SNIC-UPPMAX www.uppmax.uu.se Developer at Dept of Pharm Biosciences www.farmbio.uu.se
Samual, 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. Alex -----Oorspronkelijk bericht----- Van: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] Namens Samuel Lampa Verzonden: zondag 16 december 2012 23:14 Aan: Peter Cock CC: galaxy-dev@lists.bx.psu.edu 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 <samuel.lampa@gmail.com> 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. Best // Samuel -- Developer at SNIC-UPPMAX www.uppmax.uu.se Developer at Dept of Pharm Biosciences www.farmbio.uu.se ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Alex, xvfb http://www.xfree86.org/4.0.1/Xvfb.1.html 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 <Alex.Bossers@wur.nl> wrote:
Samual, 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. Alex
-----Oorspronkelijk bericht----- Van: galaxy-dev-bounces@lists.bx.psu.edu [mailto: galaxy-dev-bounces@lists.bx.psu.edu] Namens Samuel Lampa Verzonden: zondag 16 december 2012 23:14 Aan: Peter Cock CC: galaxy-dev@lists.bx.psu.edu 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 <samuel.lampa@gmail.com> 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.
Best // Samuel
Ross, Thanks! I will check it out. Alex Van: Ross [mailto:ross.lazarus@gmail.com] Verzonden: donderdag 20 december 2012 9:52 Aan: Bossers, Alex CC: Samuel Lampa; galaxy-dev@lists.bx.psu.edu Onderwerp: Re: [galaxy-dev] Integrating generated graphics from cli tool? Alex, xvfb http://www.xfree86.org/4.0.1/Xvfb.1.html 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 <Alex.Bossers@wur.nl<mailto:Alex.Bossers@wur.nl>> wrote: Samual, 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. Alex -----Oorspronkelijk bericht----- Van: galaxy-dev-bounces@lists.bx.psu.edu<mailto:galaxy-dev-bounces@lists.bx.psu.edu> [mailto:galaxy-dev-bounces@lists.bx.psu.edu<mailto:galaxy-dev-bounces@lists.bx.psu.edu>] Namens Samuel Lampa Verzonden: zondag 16 december 2012 23:14 Aan: Peter Cock CC: galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu> 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 <samuel.lampa@gmail.com<mailto:samuel.lampa@gmail.com>> 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. Best // Samuel
participants (4)
-
Bossers, Alex -
Peter Cock -
Ross -
Samuel Lampa