Re: [galaxy-dev] FastQC Tool Errors
Hello, We are having trouble running FastQC on our production server. The original stacktrace looked like this; Fastq failed. Error executing FastQC. Unknown option: djava.awt.headless Exception in thread main java.lang.NoClassDefFoundError: uk/ac/bbsrc/babraham/FastQC/FastQCApplication Caused by: java.lang.ClassNotFoundException: uk.ac.bbsrc.babraham.FastQC.FastQCApplication at java.net.URLClassLoader$1.run(URLClassLoader.java:200) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:188) at java.lang.ClassLoader.loadClass(ClassLoader.java:307) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301) at java.lang.ClassLoader.loadClass(ClassLoader.java:252) at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:320) Could not find the main class: uk.ac.bbsrc.babraham.FastQC.FastQCApplication. Program will exit. Then I tried to update java to the most current version. The current version is java -version java version 1.7.0_05 Java(TM) SE Runtime Environment (build 1.7.0_05-b06) Java HotSpot(TM) 64-Bit Server VM (build 23.1-b03, mixed mode) This changed the error message we got when we ran FastQC. The new trace looks like this; Fastq failed. Error executing FastQC. Unknown option: djava.awt.headless Error: Could not find or load main class uk.ac.bbsrc.babraham.FastQC.FastQCApplication The strange thing is that the tools works on our test server, which is almost an exact copy of the production server. -Rob __ Sure enough, this fixed the problem. I just installed the latest Sun JRE and it is working now. Thanks for the suggestion! I would have never guessed. -Josh On Mon, Jun 25, 2012 at 11:34 AM, simon andrews [hidden email]http://dev.list.galaxyproject.org/user/SendEmail.jtp?type=nodenode=4655462i=0 wrote: Yes, that's the broken version of gcj. I don't have a Centos machine here at the moment, but I think if you install OpenJDK and use the alternatives system to select that as the default JRE then that should fix things. Simon. On 25 Jun 2012, at 17:19, Josh Nielsen wrote: Hi Simon, I recently installed Java with the yum package manager on our compute nodes, and our cluster is a Centos 6 environment. Here is what the results of java -version returned on the compute nodes: *bash# java -version* *java version 1.5.0* *gij (GNU libgcj) version 4.4.4 20100726 (Red Hat 4.4.4-13)* * * *Copyright (C) 2007 Free Software Foundation, Inc.* *This is free software; see the source for copying conditions. There is NO* *warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE* . Is this version of Java too old? Perhaps I need to install the JRE manually? Thanks! On *Sat Jun 23 04:20:53 EDT 2012*, Simon Andrews [hidden email]http://dev.list.galaxyproject.org/user/SendEmail.jtp?type=nodenode=4655462i=1 wrote: Are you by any chance running an older version of gcj as your java version? There is a known bug in some of these where they don't correctly configure the headless environment, even if the correct parameters are passed. This causes exactly the kind of errors you're seeing. If this is the case you'll need to install a more recent JRE (or update your path to point to one which is already present). Simon. On Sat, Jun 23, 2012 at 6:30 AM, Josh Nielsen [hidden email]http://dev.list.galaxyproject.org/user/SendEmail.jtp?type=nodenode=4655462i=2 wrote: Hello, I am having an issue with getting the FastQC tool to work with Galaxy on our server. I downloaded the FastQC files (version 0.8.0) and changed the directory that the wrapper script looks for the 'fastqc' executable in, but when we run a job with it we have been getting the following output: Started analysis of Clip Approx 5% complete for Clip Approx 10% complete for Clip ... ... Approx 95% complete for Clip Approx 100% complete for Clip Analysis complete for Clip (.:9754): Gtk-WARNING **: cannot open display: And then the job shows as failed in Galaxy. The output .dat file just has that same output/error message in it (though it seems to indicate it got to 100%). Also when I try to execute the fastqc file directly (albeit with no arguments) I get this: Exception in thread main java.awt.HeadlessException: No X11 DISPLAY variable was set, but this program performed an operation which requires it. at java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:173) at java.awt.Window.init(Window.java:437) at java.awt.Frame.init(Frame.java:419) at java.awt.Frame.init(Frame.java:384) at javax.swing.JFrame.init(JFrame.java:174) at uk.ac.bbsrc.babraham.FastQC.FastQCApplication.init(FastQCApplication.java:271) at uk.ac.bbsrc.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:102) Both errors seem to have something to do with the graphical GUI
Re: [galaxy-dev] FastQC Tool Errors
Sure enough, this fixed the problem. I just installed the latest Sun JRE and it is working now. Thanks for the suggestion! I would have never guessed. -Josh On Mon, Jun 25, 2012 at 11:34 AM, simon andrews simon.andr...@babraham.ac.uk wrote: Yes, that's the broken version of gcj. I don't have a Centos machine here at the moment, but I think if you install OpenJDK and use the alternatives system to select that as the default JRE then that should fix things. Simon. On 25 Jun 2012, at 17:19, Josh Nielsen wrote: Hi Simon, I recently installed Java with the yum package manager on our compute nodes, and our cluster is a Centos 6 environment. Here is what the results of java -version returned on the compute nodes: *bash# java -version* *java version 1.5.0* *gij (GNU libgcj) version 4.4.4 20100726 (Red Hat 4.4.4-13)* * * *Copyright (C) 2007 Free Software Foundation, Inc.* *This is free software; see the source for copying conditions. There is NO* *warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE*. Is this version of Java too old? Perhaps I need to install the JRE manually? Thanks! On *Sat Jun 23 04:20:53 EDT 2012*, Simon Andrews simon.andr...@babraham.ac.uk galaxy-dev%40lists.bx.psu.edu?Subject=Re%3A%20%5Bgalaxy-dev%5D%20FastQC%20Tool%20ErrorsIn-Reply-To=%3CD9909700-8628-4478-814C-449803EE45F1%40babraham.ac.uk%3E wrote: Are you by any chance running an older version of gcj as your java version? There is a known bug in some of these where they don't correctly configure the headless environment, even if the correct parameters are passed. This causes exactly the kind of errors you're seeing. If this is the case you'll need to install a more recent JRE (or update your path to point to one which is already present). Simon. On Sat, Jun 23, 2012 at 6:30 AM, Josh Nielsen jniel...@hudsonalpha.com wrote: Hello, I am having an issue with getting the FastQC tool to work with Galaxy on our server. I downloaded the FastQC files (version 0.8.0) and changed the directory that the wrapper script looks for the 'fastqc' executable in, but when we run a job with it we have been getting the following output: Started analysis of Clip Approx 5% complete for Clip Approx 10% complete for Clip ... ... Approx 95% complete for Clip Approx 100% complete for Clip Analysis complete for Clip (.:9754): Gtk-WARNING **: cannot open display: And then the job shows as failed in Galaxy. The output .dat file just has that same output/error message in it (though it seems to indicate it got to 100%). Also when I try to execute the fastqc file directly (albeit with no arguments) I get this: Exception in thread main java.awt.HeadlessException: No X11 DISPLAY variable was set, but this program performed an operation which requires it. at java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:173) at java.awt.Window.init(Window.java:437) at java.awt.Frame.init(Frame.java:419) at java.awt.Frame.init(Frame.java:384) at javax.swing.JFrame.init(JFrame.java:174) at uk.ac.bbsrc.babraham.FastQC.FastQCApplication.init(FastQCApplication.java:271) at uk.ac.bbsrc.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:102) Both errors seem to have something to do with the graphical GUI component of FastQC (which I have seen some screenshots for on the FastQC webpage). If this application is GUI-driven how did the online PSU Galaxy get it to work with their wrapper script when the tools are run in a command-line environment with no X11 or Gtk? Essentially I'm just wondering what steps I'm missing here to getting this to work with our Galaxy mirror, other than just dropping the executable in place? Any suggestions? Thanks, Josh ___ 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/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444; The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT *Registered Charity No. 1053902.* The information transmitted in this email is directed only to the addressee. If you received this in error, please contact the sender and delete this email from your system. The contents of this e-mail are the views of the sender and do not necessarily represent the views of the Babraham Institute. Full conditions at: www.babraham.ac.ukhttp://www.babraham.ac.uk/email_disclaimer.html ___ 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
Re: [galaxy-dev] FastQC Tool Errors
Yes, that's the broken version of gcj. I don't have a Centos machine here at the moment, but I think if you install OpenJDK and use the alternatives system to select that as the default JRE then that should fix things. Simon. On 25 Jun 2012, at 17:19, Josh Nielsen wrote: Hi Simon, I recently installed Java with the yum package manager on our compute nodes, and our cluster is a Centos 6 environment. Here is what the results of java -version returned on the compute nodes: bash# java -version java version 1.5.0 gij (GNU libgcj) version 4.4.4 20100726 (Red Hat 4.4.4-13) Copyright (C) 2007 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. Is this version of Java too old? Perhaps I need to install the JRE manually? Thanks! On Sat Jun 23 04:20:53 EDT 2012, Simon Andrews simon.andr...@babraham.ac.uk mailto:galaxy-dev%40lists.bx.psu.edu?Subject=Re%3A%20%5Bgalaxy-dev%5D%20FastQC%20Tool%20ErrorsIn-Reply-To=%3CD9909700-8628-4478-814C-449803EE45F1%40babraham.ac.uk%3E wrote: Are you by any chance running an older version of gcj as your java version? There is a known bug in some of these where they don't correctly configure the headless environment, even if the correct parameters are passed. This causes exactly the kind of errors you're seeing. If this is the case you'll need to install a more recent JRE (or update your path to point to one which is already present). Simon. On Sat, Jun 23, 2012 at 6:30 AM, Josh Nielsen jniel...@hudsonalpha.commailto:jniel...@hudsonalpha.com wrote: Hello, I am having an issue with getting the FastQC tool to work with Galaxy on our server. I downloaded the FastQC files (version 0.8.0) and changed the directory that the wrapper script looks for the 'fastqc' executable in, but when we run a job with it we have been getting the following output: Started analysis of Clip Approx 5% complete for Clip Approx 10% complete for Clip ... ... Approx 95% complete for Clip Approx 100% complete for Clip Analysis complete for Clip (.:9754): Gtk-WARNING **: cannot open display: And then the job shows as failed in Galaxy. The output .dat file just has that same output/error message in it (though it seems to indicate it got to 100%). Also when I try to execute the fastqc file directly (albeit with no arguments) I get this: Exception in thread main java.awt.HeadlessException: No X11 DISPLAY variable was set, but this program performed an operation which requires it. at java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:173) at java.awt.Window.init(Window.java:437) at java.awt.Frame.init(Frame.java:419) at java.awt.Frame.init(Frame.java:384) at javax.swing.JFrame.init(JFrame.java:174) at uk.ac.bbsrc.babraham.FastQC.FastQCApplication.init(FastQCApplication.java:271) at uk.ac.bbsrc.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:102) Both errors seem to have something to do with the graphical GUI component of FastQC (which I have seen some screenshots for on the FastQC webpage). If this application is GUI-driven how did the online PSU Galaxy get it to work with their wrapper script when the tools are run in a command-line environment with no X11 or Gtk? Essentially I'm just wondering what steps I'm missing here to getting this to work with our Galaxy mirror, other than just dropping the executable in place? Any suggestions? Thanks, Josh ___ 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/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444tel:%2B61%20385321444; The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT Registered Charity No. 1053902. The information transmitted in this email is directed only to the addressee. If you received this in error, please contact the sender and delete this email from your system. The contents of this e-mail are the views of the sender and do not necessarily represent the views of the Babraham Institute. Full conditions at: www.babraham.ac.ukhttp://www.babraham.ac.uk/email_disclaimer.html ___ 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/
Re: [galaxy-dev] FastQC Tool Errors
Are you by any chance running an older version of gcj as your java version? There is a known bug in some of these where they don't correctly configure the headless environment, even if the correct parameters are passed. This causes exactly the kind of errors you're seeing. If this is the case you'll need to install a more recent JRE (or update your path to point to one which is already present). Simon. On 22 Jun 2012, at 23:35, Ross wrote: Do you run an X11 virtual frame buffer - eg Xvfb? Otherwise AFAIK R graphics and Java will complain on headless nodes. On Sat, Jun 23, 2012 at 6:30 AM, Josh Nielsen jniel...@hudsonalpha.com wrote: Hello, I am having an issue with getting the FastQC tool to work with Galaxy on our server. I downloaded the FastQC files (version 0.8.0) and changed the directory that the wrapper script looks for the 'fastqc' executable in, but when we run a job with it we have been getting the following output: Started analysis of Clip Approx 5% complete for Clip Approx 10% complete for Clip ... ... Approx 95% complete for Clip Approx 100% complete for Clip Analysis complete for Clip (.:9754): Gtk-WARNING **: cannot open display: And then the job shows as failed in Galaxy. The output .dat file just has that same output/error message in it (though it seems to indicate it got to 100%). Also when I try to execute the fastqc file directly (albeit with no arguments) I get this: Exception in thread main java.awt.HeadlessException: No X11 DISPLAY variable was set, but this program performed an operation which requires it. at java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:173) at java.awt.Window.init(Window.java:437) at java.awt.Frame.init(Frame.java:419) at java.awt.Frame.init(Frame.java:384) at javax.swing.JFrame.init(JFrame.java:174) at uk.ac.bbsrc.babraham.FastQC.FastQCApplication.init(FastQCApplication.java:271) at uk.ac.bbsrc.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:102) Both errors seem to have something to do with the graphical GUI component of FastQC (which I have seen some screenshots for on the FastQC webpage). If this application is GUI-driven how did the online PSU Galaxy get it to work with their wrapper script when the tools are run in a command-line environment with no X11 or Gtk? Essentially I'm just wondering what steps I'm missing here to getting this to work with our Galaxy mirror, other than just dropping the executable in place? Any suggestions? Thanks, Josh ___ 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/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444; ___ 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/ The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT Registered Charity No. 1053902. The information transmitted in this email is directed only to the addressee. If you received this in error, please contact the sender and delete this email from your system. The contents of this e-mail are the views of the sender and do not necessarily represent the views of the Babraham Institute. Full conditions at: www.babraham.ac.ukhttp://www.babraham.ac.uk/email_disclaimer.html ___ 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/
Re: [galaxy-dev] FastQC Tool Errors
We are not currently running anything like Xvfb, but if that is the only way to get it to run I suppose I can try it. How does PSU's Galaxy handle grabbing the results and outputting them to Galaxy without having X11 applications (useless/unneeded with Galaxy - meant for manual thickclient GUI interaction not browsers) starting on the servers on their end for every user job executed? And how do they kill or manage the opened X11 sessions once started? The users do not/aren't supposed to see the X11 / R Graphics, correct? They are only supposed to see whatever file output it results in so that they can view it strictly through Galaxy, as per the wrapper's text description: The tool produces a single HTML output file that contains all of the results. It is only the results summary in HTML that Galaxy the user are concerned about, as I understand it. We run Galaxy on a Linux cluster headnode (with no monitor only boots to init 3 [no GUI] - with admin-only ssh access) and it submits all jobs to the compute nodes and then returns the results. I installed Java on each compute nodes but do I now need to install that X11 virtual frame buffer/Xvfb on all of the compute nodes also? Thanks! On Fri, Jun 22, 2012 at 5:35 PM, Ross ross.laza...@gmail.com wrote: Do you run an X11 virtual frame buffer - eg Xvfb? Otherwise AFAIK R graphics and Java will complain on headless nodes. On Sat, Jun 23, 2012 at 6:30 AM, Josh Nielsen jniel...@hudsonalpha.com wrote: Hello, I am having an issue with getting the FastQC tool to work with Galaxy on our server. I downloaded the FastQC files (version 0.8.0) and changed the directory that the wrapper script looks for the 'fastqc' executable in, but when we run a job with it we have been getting the following output: Started analysis of Clip Approx 5% complete for Clip Approx 10% complete for Clip ... ... Approx 95% complete for Clip Approx 100% complete for Clip Analysis complete for Clip (.:9754): Gtk-WARNING **: cannot open display: And then the job shows as failed in Galaxy. The output .dat file just has that same output/error message in it (though it seems to indicate it got to 100%). Also when I try to execute the fastqc file directly (albeit with no arguments) I get this: Exception in thread main java.awt.HeadlessException: No X11 DISPLAY variable was set, but this program performed an operation which requires it. at java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:173) at java.awt.Window.init(Window.java:437) at java.awt.Frame.init(Frame.java:419) at java.awt.Frame.init(Frame.java:384) at javax.swing.JFrame.init(JFrame.java:174) at uk.ac.bbsrc.babraham.FastQC.FastQCApplication.init(FastQCApplication.java:271) at uk.ac.bbsrc.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:102) Both errors seem to have something to do with the graphical GUI component of FastQC (which I have seen some screenshots for on the FastQC webpage). If this application is GUI-driven how did the online PSU Galaxy get it to work with their wrapper script when the tools are run in a command-line environment with no X11 or Gtk? Essentially I'm just wondering what steps I'm missing here to getting this to work with our Galaxy mirror, other than just dropping the executable in place? Any suggestions? Thanks, Josh ___ 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/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444; ___ 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/
Re: [galaxy-dev] FastQC Tool Errors
Hi Simon, I recently installed Java with the yum package manager on our compute nodes, and our cluster is a Centos 6 environment. Here is what the results of java -version returned on the compute nodes: *bash# java -version* *java version 1.5.0* *gij (GNU libgcj) version 4.4.4 20100726 (Red Hat 4.4.4-13)* * * *Copyright (C) 2007 Free Software Foundation, Inc.* *This is free software; see the source for copying conditions. There is NO* *warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE* . Is this version of Java too old? Perhaps I need to install the JRE manually? Thanks! On *Sat Jun 23 04:20:53 EDT 2012*, Simon Andrews simon.andr...@babraham.ac.uk galaxy-dev%40lists.bx.psu.edu?Subject=Re%3A%20%5Bgalaxy-dev%5D%20FastQC%20Tool%20ErrorsIn-Reply-To=%3CD9909700-8628-4478-814C-449803EE45F1%40babraham.ac.uk%3E wrote: Are you by any chance running an older version of gcj as your java version? There is a known bug in some of these where they don't correctly configure the headless environment, even if the correct parameters are passed. This causes exactly the kind of errors you're seeing. If this is the case you'll need to install a more recent JRE (or update your path to point to one which is already present). Simon. On Sat, Jun 23, 2012 at 6:30 AM, Josh Nielsen jniel...@hudsonalpha.com wrote: Hello, I am having an issue with getting the FastQC tool to work with Galaxy on our server. I downloaded the FastQC files (version 0.8.0) and changed the directory that the wrapper script looks for the 'fastqc' executable in, but when we run a job with it we have been getting the following output: Started analysis of Clip Approx 5% complete for Clip Approx 10% complete for Clip ... ... Approx 95% complete for Clip Approx 100% complete for Clip Analysis complete for Clip (.:9754): Gtk-WARNING **: cannot open display: And then the job shows as failed in Galaxy. The output .dat file just has that same output/error message in it (though it seems to indicate it got to 100%). Also when I try to execute the fastqc file directly (albeit with no arguments) I get this: Exception in thread main java.awt.HeadlessException: No X11 DISPLAY variable was set, but this program performed an operation which requires it. at java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:173) at java.awt.Window.init(Window.java:437) at java.awt.Frame.init(Frame.java:419) at java.awt.Frame.init(Frame.java:384) at javax.swing.JFrame.init(JFrame.java:174) at uk.ac.bbsrc.babraham.FastQC.FastQCApplication.init(FastQCApplication.java:271) at uk.ac.bbsrc.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:102) Both errors seem to have something to do with the graphical GUI component of FastQC (which I have seen some screenshots for on the FastQC webpage). If this application is GUI-driven how did the online PSU Galaxy get it to work with their wrapper script when the tools are run in a command-line environment with no X11 or Gtk? Essentially I'm just wondering what steps I'm missing here to getting this to work with our Galaxy mirror, other than just dropping the executable in place? Any suggestions? Thanks, Josh ___ 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/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444; ___ 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/
Re: [galaxy-dev] FastQC Tool Errors
Thanks Simon! I'll definitely give that a shot. -Josh On Mon, Jun 25, 2012 at 11:34 AM, simon andrews simon.andr...@babraham.ac.uk wrote: Yes, that's the broken version of gcj. I don't have a Centos machine here at the moment, but I think if you install OpenJDK and use the alternatives system to select that as the default JRE then that should fix things. Simon. On 25 Jun 2012, at 17:19, Josh Nielsen wrote: Hi Simon, I recently installed Java with the yum package manager on our compute nodes, and our cluster is a Centos 6 environment. Here is what the results of java -version returned on the compute nodes: *bash# java -version* *java version 1.5.0* *gij (GNU libgcj) version 4.4.4 20100726 (Red Hat 4.4.4-13)* * * *Copyright (C) 2007 Free Software Foundation, Inc.* *This is free software; see the source for copying conditions. There is NO* *warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE*. Is this version of Java too old? Perhaps I need to install the JRE manually? Thanks! On *Sat Jun 23 04:20:53 EDT 2012*, Simon Andrews simon.andr...@babraham.ac.uk galaxy-dev%40lists.bx.psu.edu?Subject=Re%3A%20%5Bgalaxy-dev%5D%20FastQC%20Tool%20ErrorsIn-Reply-To=%3CD9909700-8628-4478-814C-449803EE45F1%40babraham.ac.uk%3E wrote: Are you by any chance running an older version of gcj as your java version? There is a known bug in some of these where they don't correctly configure the headless environment, even if the correct parameters are passed. This causes exactly the kind of errors you're seeing. If this is the case you'll need to install a more recent JRE (or update your path to point to one which is already present). Simon. On Sat, Jun 23, 2012 at 6:30 AM, Josh Nielsen jniel...@hudsonalpha.com wrote: Hello, I am having an issue with getting the FastQC tool to work with Galaxy on our server. I downloaded the FastQC files (version 0.8.0) and changed the directory that the wrapper script looks for the 'fastqc' executable in, but when we run a job with it we have been getting the following output: Started analysis of Clip Approx 5% complete for Clip Approx 10% complete for Clip ... ... Approx 95% complete for Clip Approx 100% complete for Clip Analysis complete for Clip (.:9754): Gtk-WARNING **: cannot open display: And then the job shows as failed in Galaxy. The output .dat file just has that same output/error message in it (though it seems to indicate it got to 100%). Also when I try to execute the fastqc file directly (albeit with no arguments) I get this: Exception in thread main java.awt.HeadlessException: No X11 DISPLAY variable was set, but this program performed an operation which requires it. at java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:173) at java.awt.Window.init(Window.java:437) at java.awt.Frame.init(Frame.java:419) at java.awt.Frame.init(Frame.java:384) at javax.swing.JFrame.init(JFrame.java:174) at uk.ac.bbsrc.babraham.FastQC.FastQCApplication.init(FastQCApplication.java:271) at uk.ac.bbsrc.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:102) Both errors seem to have something to do with the graphical GUI component of FastQC (which I have seen some screenshots for on the FastQC webpage). If this application is GUI-driven how did the online PSU Galaxy get it to work with their wrapper script when the tools are run in a command-line environment with no X11 or Gtk? Essentially I'm just wondering what steps I'm missing here to getting this to work with our Galaxy mirror, other than just dropping the executable in place? Any suggestions? Thanks, Josh ___ 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/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444; The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT *Registered Charity No. 1053902.* The information transmitted in this email is directed only to the addressee. If you received this in error, please contact the sender and delete this email from your system. The contents of this e-mail are the views of the sender and do not necessarily represent the views of the Babraham Institute. Full conditions at: www.babraham.ac.ukhttp://www.babraham.ac.uk/email_disclaimer.html ___ 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/
[galaxy-dev] FastQC Tool Errors
Hello, I am having an issue with getting the FastQC tool to work with Galaxy on our server. I downloaded the FastQC files (version 0.8.0) and changed the directory that the wrapper script looks for the 'fastqc' executable in, but when we run a job with it we have been getting the following output: Started analysis of Clip Approx 5% complete for Clip Approx 10% complete for Clip ... ... Approx 95% complete for Clip Approx 100% complete for Clip Analysis complete for Clip (.:9754): Gtk-WARNING **: cannot open display: And then the job shows as failed in Galaxy. The output .dat file just has that same output/error message in it (though it seems to indicate it got to 100%). Also when I try to execute the fastqc file directly (albeit with no arguments) I get this: Exception in thread main java.awt.HeadlessException: No X11 DISPLAY variable was set, but this program performed an operation which requires it. at java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:173) at java.awt.Window.init(Window.java:437) at java.awt.Frame.init(Frame.java:419) at java.awt.Frame.init(Frame.java:384) at javax.swing.JFrame.init(JFrame.java:174) at uk.ac.bbsrc.babraham.FastQC.FastQCApplication.init(FastQCApplication.java:271) at uk.ac.bbsrc.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:102) Both errors seem to have something to do with the graphical GUI component of FastQC (which I have seen some screenshots for on the FastQC webpage). If this application is GUI-driven how did the online PSU Galaxy get it to work with their wrapper script when the tools are run in a command-line environment with no X11 or Gtk? Essentially I'm just wondering what steps I'm missing here to getting this to work with our Galaxy mirror, other than just dropping the executable in place? Any suggestions? Thanks, Josh ___ 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/
Re: [galaxy-dev] FastQC Tool Errors
Do you run an X11 virtual frame buffer - eg Xvfb? Otherwise AFAIK R graphics and Java will complain on headless nodes. On Sat, Jun 23, 2012 at 6:30 AM, Josh Nielsen jniel...@hudsonalpha.com wrote: Hello, I am having an issue with getting the FastQC tool to work with Galaxy on our server. I downloaded the FastQC files (version 0.8.0) and changed the directory that the wrapper script looks for the 'fastqc' executable in, but when we run a job with it we have been getting the following output: Started analysis of Clip Approx 5% complete for Clip Approx 10% complete for Clip ... ... Approx 95% complete for Clip Approx 100% complete for Clip Analysis complete for Clip (.:9754): Gtk-WARNING **: cannot open display: And then the job shows as failed in Galaxy. The output .dat file just has that same output/error message in it (though it seems to indicate it got to 100%). Also when I try to execute the fastqc file directly (albeit with no arguments) I get this: Exception in thread main java.awt.HeadlessException: No X11 DISPLAY variable was set, but this program performed an operation which requires it. at java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:173) at java.awt.Window.init(Window.java:437) at java.awt.Frame.init(Frame.java:419) at java.awt.Frame.init(Frame.java:384) at javax.swing.JFrame.init(JFrame.java:174) at uk.ac.bbsrc.babraham.FastQC.FastQCApplication.init(FastQCApplication.java:271) at uk.ac.bbsrc.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:102) Both errors seem to have something to do with the graphical GUI component of FastQC (which I have seen some screenshots for on the FastQC webpage). If this application is GUI-driven how did the online PSU Galaxy get it to work with their wrapper script when the tools are run in a command-line environment with no X11 or Gtk? Essentially I'm just wondering what steps I'm missing here to getting this to work with our Galaxy mirror, other than just dropping the executable in place? Any suggestions? Thanks, Josh ___ 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/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444; ___ 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/
