DeNovoGUI about specs

[mvaudel]

Wow that was really impressive, you are a magician!

[ypriverol]

@prvst @hbarsnes Is this issue solve?

[hbarsnes]

@prvst @hbarsnes Is this issue solve?

I think so. Please update to the latest DeNovoGUI version (v1.10.4) to check. As you're using a version from almost a year ago.

[ypriverol]

@hbarsnes can you do that. We are moving forward some of the containers for the publication and also the presentation in the ASMS. BTW do you have the link of the publication in google?

[prvst]

I just added the latest deNovoGUi bin to the archive and then I created a new Dockerfile for it

When I run the following command:
docker run biodckr/denovogui /usr/lib/jvm/java-7-openjdk-amd64/jre/bin/java -splash:resources/conf/denovogui-splash.png -Xms128M -Xmx4096M -cp /home/biodocker/bin/DeNovoGUI-1.5.2/DeNovoGUI-1.5.2.jar com.compomics.denovogui.gui.DeNovoGUI

I get the following message:

Error: Could not find or load main class com.compomics.denovogui.gui.DeNovoGUI

[hbarsnes]

BTW do you have the link of the publication in google?

Which publication are you referring to, the DeNovoGUI one? If so, you can find it here: http://www.ncbi.nlm.nih.gov/pubmed/24295440.

Error: Could not find or load main class com.compomics.denovogui.gui.DeNovoGUI

Using just "java -cp DeNovoGUI-1.11.0-beta.jar com.compomics.denovogui.gui.DeNovoGUI" works fine on my side if I'm in the same folder as the jar file. Using the complete path also works fine. So assume it's a problem with the "/home/biodocker/bin/DeNovoGUI-1.5.2/DeNovoGUI-1.5.2.jar" path?

[ypriverol]

@hbarsnes I'm talking about the current BioDocker publication, I will send you an invitation by email. @prvst How did you install the container? can you help @hbarsnes to install properly the content. @hbarsnes the idea is that in the future the developers maintain their own containers and help the users to use them.

[prvst]

@ypriverol @hbarsnes Download / git clone the repository containing the Dockerfile. You can work on the file to make the changes then just run docker build -t biodckr/denovogui . . Always run this on the same folder with the Dockerfile

[prvst]

@hbarsnes, @ypriverol
I added a ENV DIsplay:0 to the Dockerfile, then I ran:

docker run biodckr/denovogui java -Xms128M -Xmx4096M -cp /home/biodocker/bin/DeNovoGUI-1.10.4/DeNovoGUI-1.10.4.jar com.compomics.denovogui.gui.DeNovoGUI

and I got this:

Exception in thread "main" java.lang.InternalError: Can't connect to X11 window server using ':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:110)
at java.security.AccessController.doPrivileged(Native Method)
at sun.awt.X11GraphicsEnvironment.(X11GraphicsEnvironment.java:74)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:195)
at java.awt.GraphicsEnvironment.createGE(GraphicsEnvironment.java:102)
at java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment(GraphicsEnvironment.java:81)
at sun.awt.X11.XToolkit.(XToolkit.java:120)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:195)
at java.awt.Toolkit$2.run(Toolkit.java:869)
at java.security.AccessController.doPrivileged(Native Method)
at java.awt.Toolkit.getDefaultToolkit(Toolkit.java:861)
at sun.swing.SwingUtilities2.getSystemMnemonicKeyMask(SwingUtilities2.java:1928)
at javax.swing.plaf.basic.BasicLookAndFeel.initComponentDefaults(BasicLookAndFeel.java:752)
at javax.swing.plaf.metal.MetalLookAndFeel.initComponentDefaults(MetalLookAndFeel.java:434)
at javax.swing.plaf.basic.BasicLookAndFeel.getDefaults(BasicLookAndFeel.java:148)
at javax.swing.plaf.metal.MetalLookAndFeel.getDefaults(MetalLookAndFeel.java:1589)
at javax.swing.UIManager.setLookAndFeel(UIManager.java:536)
at javax.swing.UIManager.setLookAndFeel(UIManager.java:576)
at javax.swing.UIManager.initializeDefaultLAF(UIManager.java:1345)
at javax.swing.UIManager.initialize(UIManager.java:1455)
at javax.swing.UIManager.maybeInitialize(UIManager.java:1422)
at javax.swing.UIManager.getInstalledLookAndFeels(UIManager.java:416)
at com.compomics.util.gui.UtilitiesGUIDefaults.setLookAndFeel(UtilitiesGUIDefaults.java:32)
at com.compomics.denovogui.gui.DeNovoGUI.main(DeNovoGUI.java:2188)

Last time I checked, the same thing was happening with SearchGUI

[hbarsnes]

@prvst @ypriverol If you run DeNovoGUI (or SearchGUI) in GUI mode you need an environment that support graphical components. I have very little experience with X11 and its errors though, so I'm afraid I cannot be of much help interpreting the above error. The code works fine if run on a "normal" Linux setup though.

[mvaudel]

I think the main use case of containers would be command line to create projects and integrate tools in pipelines. The results can be subsequently downloaded and visualized on a desktop machine. At least for a first step if you get the CLI to run that is more than enough :)

[ypriverol]

I agree, but if this is the case them we need to define @prvst a way that let the users know that this is only command line option. We have the same problem in other containers like OpenMS containers.

[mvaudel]

yup, is that a general UI problem or just on some applications?

[prvst]

@ypriverol @mvaudel @hbarsnes

I have some really cool news, I found out how to run it! I just did a complete analysis from data loading to saving, using DeNovoGUI, running Novor. The entire process was made by tunneling the GUI from inside the container to my host desktop.

here is the command you need to run:

docker run -ti --rm -e DISPLAY=$DISPLAY -v /tmp/.X11-unix:/tmp/.X11-unix -v /data/felipevl/projects/h2s/:/data/ biodckr/dnvgui java -jar /home/biodocker/bin/DeNovoGUI-1.10.4/DeNovoGUI-1.10.4.jar

The secret here is to share the X11 configuration from the host into the container, so for that we need two -v parameters on the execution string, one for the X11 settings and the other for our files. Also, the container needs the $DISPLAY env var from host.

This is really cool, but I also agree with @mvaudel about the CLI and the possibility to integrate this component into pipelines.

Now I will test this with SearchGUI.

Just a side note: I'm not sure yet how to run this in a Windows host

[hbarsnes]

@prvst @ypriverol @mvaudel

I have some really cool news, I found out how to run it!

Great! Should solve the problem for SearchGUI as well I assume (and PeptideShaker if it is included at all?).

[ypriverol]

yes both of them are running now!!

[mvaudel]

Legendary! Very elegant solution!