search

BioContainers / containers

Bioinformatics containers
http://biocontainers.pro
Apache License 2.0
677 stars 248 forks source link

fastqc dont works #262

Open arturomarin opened 6 years ago

arturomarin commented 6 years ago

We are trying to use the fastqc docker installed on a server. Using a computer with windows and PuTYY we have no problem, but from Linux and Mac OS we can not use fastqc.

From the local computer we do:

$ ssh -X <user>@<Server IP>

In the server:

$ export DISPLAY=<IP of the local computer>:0.0
$ xhost +; docker run -v /home/amarin/datos_amarin/:/data/ -v /tmp/.X11-unix:/tmp/.X11-unix -e DISPLAY=$DISPLAY -it --rm biocontainers/fastqc fastqc

And the server gives us the following error:

xhost:  unable to open display "10.11.0.10:0.0"
Exception in thread "main" java.awt.AWTError: Can't connect to X11 window server using '10.11.0.10:0.0' as the value of the DISPLAY variable.
    at sun.awt.X11GraphicsEnvironment.initDisplay(Native Method)
    at sun.awt.X11GraphicsEnvironment.access$200(X11GraphicsEnvironment.java:65)
    at sun.awt.X11GraphicsEnvironment$1.run(X11GraphicsEnvironment.java:115)
    at java.security.AccessController.doPrivileged(Native Method)
    at sun.awt.X11GraphicsEnvironment.<clinit>(X11GraphicsEnvironment.java:74)
    at java.lang.Class.forName0(Native Method)
    at java.lang.Class.forName(Class.java:264)
    at java.awt.GraphicsEnvironment.createGE(GraphicsEnvironment.java:103)
    at java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment(GraphicsEnvironment.java:82)
    at sun.awt.X11.XToolkit.<clinit>(XToolkit.java:126)
    at java.lang.Class.forName0(Native Method)
    at java.lang.Class.forName(Class.java:264)
    at java.awt.Toolkit$2.run(Toolkit.java:860)
    at java.awt.Toolkit$2.run(Toolkit.java:855)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.awt.Toolkit.getDefaultToolkit(Toolkit.java:854)
    at javax.swing.UIManager.getSystemLookAndFeelClassName(UIManager.java:611)
    at uk.ac.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:322)

But the xeyes command works

Thanks in advance

osallou commented 6 years ago

I tested on my local computer (ubuntu) and it works.

sudo docker run  -v /tmp/.X11-unix:/tmp/.X11-unix -e DISPLAY=$DISPLAY -it --rm biocontainers/fastqc fastqc

xeyes works on your ?

Maybe a xauthority/x11 problem on your server.

arturomarin commented 6 years ago

Thanks, but I do not think that is because we can connect to the server without any problem. xauthority seems fine. The problem is something related to the redirection of the X, which using PuTTY does work but not on Mac / Linux.

yes, xeyes works,... but not the export of X's when using fastqc.

ypriverol commented 5 years ago

@arturomarin have you solve this issue.

arturomarin commented 5 years ago

I apologize for the delay in answering. We had problems with the server hardware and had to stop installing programs on the server. You can close the issue, and if I try again to install the program and I have problems I will post an issue.

MattBrauer commented 5 years ago

This is an issue with XQuartz permissions. see here: https://medium.com/@mreichelt/how-to-show-x11-windows-within-docker-on-mac-50759f4b65cb