[galaxy-dev] wrapping qvalue in Galaxy
Hi, I am trying to wrap the qvalue R package in a script (as I have already done for a dozen), but this time I have repeatedly the same error *In fun(libname, pkgname) : no DISPLAY variable so Tk is not available* or *Loading Tcl/Tk interface ... done* (and red, desperately red box). I already had this type of bugs and fixed them by using the suppressWarnings or suppressMessages R methods. But this time, no way. I really don't need the Tcl/Tk interface and I am not using it with qvalue... frustrating. (my code run into R in command lines like a charm) Any clue to shut off Galaxy and get this miserable pvalue vector output ? Christophe PS. I browsed the net, found traces of problems similar to mine, but unfortunately no trace of solutions. ___ 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] wrapping qvalue in Galaxy
This is probably because R on a server requires an X11 framebuffer since your process is not able to open an X11 server connection while it's running. Does http://stackoverflow.com/questions/1710853/how-to-run-r-on-a-server-without-x11-and-avoid-broken-dependencies help? On Thu, Jun 7, 2012 at 8:57 AM, Christophe Antoniewski droso...@gmail.com wrote: Hi, I am trying to wrap the qvalue R package in a script (as I have already done for a dozen), but this time I have repeatedly the same error In fun(libname, pkgname) : no DISPLAY variable so Tk is not available or Loading Tcl/Tk interface ... done (and red, desperately red box). I already had this type of bugs and fixed them by using the suppressWarnings or suppressMessages R methods. But this time, no way. I really don't need the Tcl/Tk interface and I am not using it with qvalue... frustrating. (my code run into R in command lines like a charm) Any clue to shut off Galaxy and get this miserable pvalue vector output ? Christophe PS. I browsed the net, found traces of problems similar to mine, but unfortunately no trace of solutions. ___ 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] I can't see or access pictures in FastQC
Hi, Daniel. The wrapper doesn't introduce any new dependencies other than a working FastQC install in the right place so can you please let us know what happens when you run FastQC from the command line as the user running your Galaxy processes - it should start an interactive FastQC session where you can try running a real fastq input and check that you get the HTML outputs. Once it's all working from the command line, try the tool again and let us know how that turns out please? On Thu, Jun 7, 2012 at 6:58 AM, Dorset, Daniel C daniel.dor...@vanderbilt.edu wrote: I’m running two separate instances of Galaxy on two different servers. On both servers, whenever I run FastQC, I can see the result HTML file, but none of the pictures show up. Furthermore, if I try to access the links at the bottom of the page, they don’t lead to any real files. If I look in my database/files/subfolder, I see a dataset_### file that contains the HTML info, which I am able to see in Galaxy. There is another folder named “dataset_###_files,” and all of the pictures and the FastQC results zip file are contained in there. I can access them with full read permissions, and the sizes appear correct. Has anyone else experienced this problem? ___ 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] Task Manager: This Galaxy instance is not the job manager.
yes, i've had the same error ever since the last galaxy-dist release. i previously had multiple servers and switched to the one manager, two handlers. rewrite rules didn't need to be changed. On Thu, May 24, 2012 at 8:14 AM, Sarah Diehl di...@immunbio.mpg.de wrote: ** Hi all, I have a similar, maybe related problem. I'm running a configuration as described at http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Web%20Application%20Scaling. I have three webservers, one manager and two handlers. Everything is behind an Apache and the rewrite rules are set accordingly. When I try to access Manage Jobs, I also get the error This Galaxy instance is not the job manager. If using multiple servers, please directly access the job manager instance to manage jobs.. I have set the rewrite rule for admin/jobs to point to the manager server. When I access the manager directly from localhost I get the same error, while all other servers (web and handler) throw a server error: 127.0.0.1 - - [24/May/2012:15:37:50 +0200] GET /admin/jobs HTTP/1.1 500 - - Mozilla/5.0 (X11; Linux x86_64; rv:10.0.4) Gecko/20120424 Firefox/10.0.4 Error - type 'exceptions.AttributeError': 'NoopQueue' object has no attribute 'job_lock' URL: http://localhost:8080/admin/jobs File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/web/framework/__init__.py', line 184 in decorator return func( self, trans, *args, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/web/base/controller.py', line 2428 in jobs job_lock = trans.app.job_manager.job_queue.job_lock ) AttributeError: 'NoopQueue' object has no attribute 'job_lock' Before the update everything worked fine (I also ran multiple servers then). Best regards, Sarah On 05/16/2012 10:27 PM, Dave Lin wrote: Dear Galaxy Team, I've been getting the following error for some time when I try to access the Manage Jobs Task. This Galaxy instance is not the job manager. If using multiple servers, please directly access the job manager instance to manage jobs. For debugging purposes, I'm only running the single master instance. I'm using CloudMan/Amazon EC2. I traced the code and suspect it might have something to do with an Amazon IP Address/hostname discrepancy, but am not sure how to go about fixing this. On a related note, if I can't access this page, what is the best way to clear/cancel jobs via the command line? Thanks in advance, Dave Thanks, Dave ___ 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/ ___ 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/
