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kimpenn / PIVOT

Platform for Interactive analysis and Visualization Of Transcriptomics data
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Issue installing PIVOT on Docker #12

Closed chahatupreti closed 5 years ago

chahatupreti commented 5 years ago

Hi,

I am trying to install and run Pivot using Docker (on a Mac). I installed Docker and then as mentioned in the instructions, ran docker run -p 80:3838 eturkes/pivot-docker on my terminal. The installation seemed to go fine until it stopped at -

Gnomovision version 69, Copyright (c) 2015-2018 Qin Zhu and Junhyong Kim, University of Pennsylvania. Gnomovision comes with ABSOLUTELY NO WARRANTY; for details go to https://www.gnu.org/licenses/old-licenses/gpl-2.0.en.html. This is free software, and you are welcome to redistribute it under certain conditions. Listening on http://0.0.0.0:3838

sh: 1: xdg-open: not found

And then the cursor kept blinking after that. Does anyone know how this can be resolved?

Thanks!

qinzhu commented 5 years ago

Seems certain dependencies are missing in the docker image. Maybe Emir (@eturkes) can confirm this. If your system is MacOS I suggest try the direct install method (as a package into your local R).

eturkes commented 5 years ago

Did you try visiting localhost in your browser? The rest of it seems like normal behavior. The xdg-open command error can be safely ignored, PIVOT normally tries to automatically launch a browser but the way it does it currently is not compatible with Docker. So for now you must open a browser manually and visit localhost.

chahatupreti commented 5 years ago

Hi Emir/Qin,

I did try to visit localhost, and PIVOT was running fine. Good to know that the mentioned error is benign. Thanks a lot!

On Tue, Apr 2, 2019 at 11:37 PM Emir Turkes notifications@github.com wrote:

Did you try visiting localhost in your browser? The rest of it seems like normal behavior. The xdg-open command error can be safely ignored, PIVOT normally tries to automatically launch a browser but the way it does it currently is not compatible with Docker. So for now you must open a browser manually and visit localhost.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/qinzhu/PIVOT/issues/12#issuecomment-479336751, or mute the thread https://github.com/notifications/unsubscribe-auth/AJMQqYE9awRfdi9N6ycXsjbnjhatrfY2ks5vdDABgaJpZM4cZjDa .

--

Chahat Upreti Second Year PhD student, Molecular and Cell Biology University of Texas at Dallas

eturkes commented 5 years ago

Glad it works and thanks for reporting! I'll try to remove that error or at least in the meanwhile notify other users to ignore it