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/
[galaxy-dev] Tophat Troubles
Hello, I am having an issue on the Galaxy Main server. I had reached my maximum disk space this morning. So I cleaned out some items until my space was down to 61%. I then tried to run Tophat for RNA seq and the tool is doing nothing. I know the datasets aren't too large because I would have received an error message. The job simply goes into my queue as gray and says waiting to run. Any ideas on what is going on? Thanks, Kristen Roop ___ 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] unable to start galaxy
Re-send From: izmiyati razikin [mailto:izmiy...@novaglobal.com.sg] Sent: Monday, 25 June, 2012 11:01 PM To: 'galaxy-dev@lists.bx.psu.edu' Subject: unable to start galaxy Hello, I'm having problem starting up galaxy. I'm using RHEL 5.3 which comes with python 2.4.3. So I compiled python 2.6.5. I've created a symbolic link and set it in PATH. Yet I'm unable to start galaxy. Thanks in advance for help! Fetch successful. Starting subprocess with file monitor Traceback (most recent call last): File ./scripts/paster.py, line 34, in module command.run() File /home/software/apps/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/scri pt/command.py, line 84, in run invoke(command, command_name, options, args[1:]) File /home/software/apps/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/scri pt/command.py, line 123, in invoke exit_code = runner.run(args) File /home/software/apps/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/scri pt/command.py, line 218, in run result = self.command() File /home/software/apps/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/scri pt/serve.py, line 276, in command relative_to=base, global_conf=vars) File /home/software/apps/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/scri pt/serve.py, line 313, in loadapp **kw) File /home/software/apps/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/depl oy/loadwsgi.py, line 204, in loadapp return loadobj(APP, uri, name=name, **kw) File /home/software/apps/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/depl oy/loadwsgi.py, line 224, in loadobj global_conf=global_conf) File /home/software/apps/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/depl oy/loadwsgi.py, line 248, in loadcontext global_conf=global_conf) File /home/software/apps/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/depl oy/loadwsgi.py, line 278, in _loadconfig return loader.get_context(object_type, name, global_conf) File /home/software/apps/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/depl oy/loadwsgi.py, line 413, in get_context section) File /home/software/apps/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/depl oy/loadwsgi.py, line 458, in _context_from_explicit value = import_string(found_expr) File /home/software/apps/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/depl oy/loadwsgi.py, line 18, in import_string return pkg_resources.EntryPoint.parse(x=+s).load(False) File /home/software/apps/galaxy-dist/lib/pkg_resources.py, line 1954, in load entry = __import__(self.module_name, globals(),globals(), ['__name__']) File /home/software/apps/galaxy-dist/lib/galaxy/web/buildapp.py, line 19, in module from galaxy import config, jobs, util, tools File /home/software/apps/galaxy-dist/lib/galaxy/jobs/__init__.py, line 4, in module from galaxy import util, model File /home/software/apps/galaxy-dist/lib/galaxy/model/__init__.py, line 13, in module import galaxy.datatypes.registry File /home/software/apps/galaxy-dist/lib/galaxy/datatypes/registry.py, line 6, in module import data, tabular, interval, images, sequence, qualityscore, genetics, xml, coverage, tracks, chrominfo, binary, assembly, ngsindex, wsf File /home/software/apps/galaxy-dist/lib/galaxy/datatypes/tabular.py, line 15, in module from sniff import * File /home/software/apps/galaxy-dist/lib/galaxy/datatypes/sniff.py, line 8, in module from galaxy.datatypes.binary import unsniffable_binary_formats File /home/software/apps/galaxy-dist/lib/galaxy/datatypes/binary.py, line 12, in module from bx.seq.twobit import TWOBIT_MAGIC_NUMBER, TWOBIT_MAGIC_NUMBER_SWAP, TWOBIT_MAGIC_SIZE File /home/software/apps/galaxy-dist/eggs/bx_python-0.7.0_494c2d1d68b3_rebuild1- py2.6-linux-x86_64-ucs2.egg/bx/seq/__init__.py, line 7, in module from bx.seq.core import * File /home/software/apps/galaxy-dist/eggs/bx_python-0.7.0_494c2d1d68b3_rebuild1- py2.6-linux-x86_64-ucs2.egg/bx/seq/core.py, line 10, in module import fasta, nib, qdna File /home/software/apps/galaxy-dist/eggs/bx_python-0.7.0_494c2d1d68b3_rebuild1- py2.6-linux-x86_64-ucs2.egg/bx/seq/nib.py, line 28, in module import _nib ImportError: /home/software/apps/galaxy-dist/eggs/bx_python-0.7.0_494c2d1d68b3_rebuild1-p y2.6-linux-x86_64-ucs2.egg/bx/seq/_nib.so: undefined symbol: Py_InitModule4_64 [240223 refs] [55760 refs] Rgds, Izy ___ 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] Tophat Troubles
On Jun 25, 2012, at 5:25 PM, Kristen Roop wrote: Hello, I am having an issue on the Galaxy Main server. I had reached my maximum disk space this morning. So I cleaned out some items until my space was down to 61%. I then tried to run Tophat for RNA seq and the tool is doing nothing. I know the datasets aren't too large because I would have received an error message. The job simply goes into my queue as gray and says waiting to run. Any ideas on what is going on? Hi Kristen, The cluster that runs our NGS tools is extremely busy right now. Your job is waiting for a free cluster node, not because of your disk usage. Sorry for the inconvenience, and thanks for using Galaxy. --nate Thanks, Kristen Roop ___ 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/ ___ 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] Fully Purged Histories and still 30% used
Hello again, These numbers are in-line with the disk quota limits on Main: http://wiki.g2.bx.psu.edu/Main#User_data_and_job_quotas Just as a reminder, datasets must be 'permanently deleted', not just 'deleted', in order to not count in a quota usage amount. Instructions for reviewing deleted histories to see if they are permanently deleted or not is in the wiki link I sent earlier. In short, under the History menu - Options (gear icon) - Shared Histories, and clicking on advanced search, then view - all will display all of your work, with sizes and status. The screencast on the wiki has a walk-through. The other times this has come up, a review of all has cleared up any lingering questions about where the data is. Take care, Jen Galaxy team On 6/26/12 11:18 AM, David-Georges Vitrant Phd wrote: Hi Jennifer, Thanks for the update. I'm not 100% sure anymore. I've deleted/purged histories and datasets as far as I know. It's showing 80% usage. This is on the public instance. Says i'm using 79% and 160gb so that seems a bit more correct then before. On Tue, Jun 26, 2012 at 2:12 PM, Jennifer Jackson j...@bx.psu.edu mailto:j...@bx.psu.edu wrote: Hello, Are you still having this problem? Is this on the public main instance or your own local instance? The display numbers can take up to a few hours to update on the main server, depending on load. The update time on your local install will vary depending on your configuration. If the counts still do not seem right, double checking for deleted, but not permanently deleted histories is a good place to start. Looking for deleted/hidden datasets in existing histories is also recommended. This wiki can help: http://wiki.g2.bx.psu.edu/Learn/Managing%20Datasets#Delete_vs_Delete_Permanently Best, Jen Galaxy team On 6/23/12 12:18 PM, David-Georges Vitrant Phd wrote: I hadn't found this bug anywhere. I deleted all my histories and purged them but my counter still says I have 30% used. Am I missing something? -- Thanks, ___ 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/ -- Jennifer Jackson http://galaxyproject.org -- Thanks, David-Georges Vitrant Ph.D. -- Jennifer Jackson http://galaxyproject.org ___ 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] Tophat Troubles
The cluster was busy I think, so you just have to wait for the queue to clear...On Jun 25, 2012, at 02:25 PM, Kristen Roop kristen.r...@gmail.com wrote:Hello,I am having an issue on the Galaxy Main server.I had reached my maximum disk space this morning. So I cleaned out some items until my space was down to 61%. I then tried to run Tophat for RNA seq and the tool is doing nothing. I know the datasets aren't too large because I would have received an error message. The job simply goes into my queue as gray and says waiting to run. Any ideas on what is going on?Thanks,Kristen Roop___ 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/___ 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] Are there any database test scripts?
Hi,I am still having serious issues with running galaxy workflows from the API on my installation...I am getting random files on which the workflows are run, rather than the files I select in my script.I am suspecting that my database may be corrupt...Is there any test script that can test my theory?I am running postgres and the database may have become corrupted, although running the same WF from the UI has no problems, so I still suspect the API...ThanksThon ___ 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/
