Re: [galaxy-dev] Galaxy Reports no longer functions
Hi Iry The last but one line: "socket.error: [Errno 98] Address already in use" holds probably the clue. Looks like something else is running on the same port or you didn't stop the reports server before restarting it (after the upgrade) Regards, Hans On 08/17/2012 11:08 PM, Iry Witham wrote: Hi Team, Since I upgraded to the latest galaxy-dist I can no longer get the reports interface to function. When I go to galaxy:9001 I get the following server error: An error occurred. See the error logs for more information. (Turn debug on to display exception reports here). The reports_webapp.log is as follows: python path is: /hpcdata/galaxy-setup/galaxy-dist/eggs/pycrypto-2.0.1-py2.6-linux-x86_64-ucs4.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/bx_python-0.7.1_7b95ff194725-py2.6-linux-x86_64-ucs4.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/amqplib-0.6.1-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/pexpect-2.4-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/Babel-0.9.4-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/WebHelpers-0.2-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/wchartype-0.1-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/docutils-0.7-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/Routes-1.12.3-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/Paste-1.6-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/lib, /usr/lib/python26.zip, /usr/lib64/python2.6, /usr/lib64/python2.6/plat-linux2, /usr/lib64/python2.6/lib-tk, /usr/lib64/python2.6/lib-old, /usr/lib64/python2.6/lib-dynload, /usr/lib64/python2.6/site-packages, /usr/lib64/python2.6/site-packages/Numeric, /usr/lib64/python2.6/site-packages/gtk-2.0, /usr/local/lib64/python2.6/site-packages galaxy.model.custom_types DEBUG 2012-08-07 17:13:53,219 psycopg2 egg successfully loaded for postgres dialect galaxy.web.framework.base DEBUG 2012-08-07 17:13:59,792 Enabling 'users' controller, class: Users galaxy.web.framework.base DEBUG 2012-08-07 17:13:59,815 Enabling 'system' controller, class: System galaxy.web.framework.base DEBUG 2012-08-07 17:13:59,909 Enabling 'sample_tracking' controller, class: SampleTracking galaxy.web.framework.base DEBUG 2012-08-07 17:13:59,922 Enabling 'jobs' controller, class: Jobs galaxy.web.framework.base DEBUG 2012-08-07 17:13:59,942 Enabling 'workflows' controller, class: Workflows galaxy.web.framework.base DEBUG 2012-08-07 17:13:59,947 Enabling 'root' controller, class: Report galaxy.webapps.reports.buildapp DEBUG 2012-08-07 17:13:59,950 Enabling 'httpexceptions' middleware galaxy.webapps.reports.buildapp DEBUG 2012-08-07 17:13:59,971 Enabling 'recursive' middleware /hpcdata/galaxy-setup/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/serial_number_generator.py:11: DeprecationWarning: the md5 module is deprecated; use hashlib instead import md5 galaxy.webapps.reports.buildapp DEBUG 2012-08-07 17:14:00,708 Enabling 'error' middleware galaxy.webapps.reports.buildapp DEBUG 2012-08-07 17:14:00,749 Enabling 'trans logger' middleware galaxy.webapps.reports.buildapp DEBUG 2012-08-07 17:14:00,750 Enabling 'config' middleware galaxy.webapps.reports.buildapp DEBUG 2012-08-07 17:14:00,888 Enabling 'x-forwarded-host' middleware Starting server in PID 6345. Traceback (most recent call last): File "./scripts/paster.py", line 34, in command.run() File "/hpcdata/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py", line 84, in run invoke(command, command_name, options, args[1:]) File "/hpcdata/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py", line 123, in invoke exit_code = runner.run(args) File "/hpcdata/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py", line 218, in run result = self.command() File "/hpcdata/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py", line 303, in command serve() File "/hpcdata/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py", line 287, in serve server(app) File "/hpcdata/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 151, in server_wrapper **context.local_conf) File "/hpcdata/
Re: [galaxy-dev] grouping/separating parameters on the page
On 08/17/2012 06:41 PM, Dan Tenenbaum wrote: Hello, Is there a way to do one or both of the following: 1) Group a set of related parameters together on a tool page For this we use the (unfortunately) deprecated tag set, see: http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Cpage.3E_tag_set We haven't figured out how to use the recommended "refresh_on_change" to recreate the tag functionality, ie having several differnt pages, one after the other. Regards, Hans 2) Put a separator in between related groups. I have a tool with lots of parameters. It's ok to have them all on one page but I'd like to have some space or a line between the related groups (and maybe even a header for the group) so that users know which parameters are related. Thanks, Dan ___ 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] egg distribution error when running galaxy-central
Hi Tomithy, Thanks, this worked for me too! Just to be clear for interested devs: If I run galaxy-dist on my mac it asks me to build a whole series of eggs by hand using scripts/scramble.py, and if I follow these instructions, galaxy runs. A bit tedious but trivial to do. If I run galaxy-central on my mac the same thing happens for a few dependencies, but then it gets stuck at the error I posted originally. If I run `pip install fabric` as Tomithy suggests then I get the same results as running galaxy-dist, ie galaxy works after using scramble.py a few times. If I run galaxy-central (or presumably galaxy-dist) on ubuntu it doesn't complain about any of the dependencies, doesn't get stuck, and doesn't ask me to build any eggs by hand. So I'm now wondering if, for code editing, I should use the ubuntu environment I've set up even though the code is working natively on the mac, just to avoid future complications. Cheers, Clare On 19 August 2012 21:36, Tomithy Too wrote: > Hi Clare, > > I ran into the same problem as well when I upgraded my galaxy-central > version. I am running Mac Os10.6.8 > > What I did to get use the command $ pip install fabric > > It manually fetches the latest version of fabric from pip > (http://www.pip-installer.org/en/latest/index.html) which is a package > manager from python, also its dependencies: ssh and pycrypto, which are the > components causing the problem. I think it might be due to an erroneous > version of the egg hosted on galaxy. > > Works fine after that for me. > > Cheers > Tomithy > > > > On Wed, Aug 15, 2012 at 10:55 AM, Clare Sloggett > wrote: >> >> Hi Scott, >> >> Thanks very much for this! >> >> virtualenv is ok I think: >> clare$ echo $PATH >> /Users/clare/galaxy/galaxy_central_env/bin: . >> >> which is where I set up my environment. >> >> I'm not using anything in particular outside Enthought, that I can >> think of. Enthought packages up a whole lot of things including scipy. >> >> The strange thing is that galaxy-dist runs but galaxy-central doesn't. >> So, I was hoping it would actually be a temporary bug in the egg >> distribution, but it sounds like the problem really is my environment. >> I don't understand how Enthought can be causing problems that >> virtualenv can't work around, but I've never really understood how >> python is structured in OSX! So I think it's probably worth me going >> through the effort of setting up a working environment in an ubuntu VM >> rather than running it on my Mac - I don't want to be asking you to >> pull code changes from an environment that's unusual. >> >> I'm setting it up in VirtualBox ubuntu now (which has python 2.7.1). >> So far I've pulled the code into the vm and run it, without >> virtualenv, and it gives none of the errors I see on the Mac. My plan >> is to both share the drive containing galaxy-central and share the >> network so that I can do both the editing and the browsing on my host >> machine, but if there are better ways advice is welcome! >> >> Thanks, >> Clare >> >> >> >> On 2 August 2012 07:26, Scott McManus wrote: >> > >> > I haven't been able to reproduce this yet with the instructions you >> > gave, but I'm not using the same environment. Can you give me an idea >> > of what tools you're using outside of SciPy/NumPy/Enthought stuff? >> > >> > There is the possibility that the virtualenv.py script isn't being >> > sourced correctly. We can check if it's actually using the correct >> > environment by calling "echo $PATH" and checking that the path is >> > pointing to the virtual environment. For example, I installed >> > virtualenv stuff under /home/smcmanus/clare/galaxy_env/bin, and >> > I got: >> > (galaxy_env)$ echo $PATH >> > /home/smcmanus/clare/galaxy_env/bin:/usr/local/bin: >> > >> > -Scott >> > >> > - Original Message - >> >> Hi all, >> >> >> >> I'm trying to run galaxy-central on my laptop in order to play around >> >> with some changes, and I'm having trouble getting it to run. I can >> >> run >> >> galaxy-dist without problems and have been working with that (so its >> >> eggs are all installed already), but now I want to create a pull >> >> request so want to run galaxy-dist. I'm not trying to install any >> >> extra tools or data, just the code. >> >> >> >> I'm running on OSX 10.7.4 and using virtualenv. I have Enthought >> >> installed, and I assume I will be using its version of python by >> >> default. The default python seems to be 2.7.3. >> >> >> >> I'm using the same virtualenv environment for galaxy-dist and >> >> galaxy-central (though it doesn't seem to matter if I give >> >> galaxy-central its own environment, I see the same error). So the >> >> steps were: >> >> - create a virtualenv environment and activate it >> >> - get galaxy-dist and call run.sh - it asked me to build quite a lot >> >> of dependencies myself, which was just a matter of running the >> >> requested commands, and then it worked with no problems. >> >> - shut down galaxy-dist, and in a
[galaxy-dev] Backup_strategies_for_Galaxy
Hi, We are in the process of deploying a small Galaxy server here at Texas A&M University I am a GNU/Linux kind of guy My IT people want to use an SMB-mounted drive share as a backup destination I am concerned that this might impact the performance of the server as in my mind the equation is as follows: SMB=Microsoft=windows=not_GNU/Linux=bad_Idea But then again I am a geneticist Any comments and/or other ideas?? Thanks --Rodolfo ___ 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] Trackster Bug
This bug has been fixed in galaxy-central changeset 0b58ac6510c5 Thanks for reporting, J. On Aug 15, 2012, at 5:41 AM, SHAUN WEBB wrote: > > Hi, not sure if this has been reported yet. > > If I use the dataset icon to view in trackster then select view in saved > visualisation, the saved visualisations pop up momentarily then the window > closes. > > I've tested this on the main galaxy site and my own instance on Chrome and > Firefox. > > Thanks > Shaun Webb > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > > ___ > 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] FTP upload - symlink to uploaded data
On Aug 17, 2012, at 3:17 AM, Joachim Jacob wrote: > Hi Nate, > > thanks. Do you know what's the reason for using copying first the contents to > the /tmp directory, before copying it into a the database/files/... Seems > inefficient to do so, or is this not how it works perhaps? Hi Joachim, If you set new_file_path in universe_wsgi.ini to be on the same filesystem as your FTP upload directory, there should not be any copying necessary. Thanks, --nate > > Regards, > Joachim > > Joachim Jacob, PhD > > Rijvisschestraat 120, 9052 Zwijnaarde > Tel: +32 9 244.66.34 > Bioinformatics Training and Services (BITS) > http://www.bits.vib.be > @bitsatvib > > On 08/16/2012 05:19 PM, Nate Coraor wrote: >> On Aug 16, 2012, at 11:09 AM, Joachim Jacob wrote: >> >>> Excuses for the repost, but I really need to solve this. >>> >>> Uploading with FTP fails on our Galaxy, because the /tmp directory has not >>> enough space. How can I hack in the Galaxy code base that the temporary >>> directory needs to be /mnt/galaxydb/tmp ? Another solution: how can I >>> provide a symlink to our FTP directory? >> Hi Joachim, >> >> It's not possible with the FTP upload method, but if you set >> user_library_import_dir in the config file, users can upload files from a >> server directory and choose the "link" option, just like an admin can. >> >> --nate >> >>> >>> Thanks for any hint, >>> >>> Joachim >>> >>> >>> Joachim Jacob, PhD >>> >>> Rijvisschestraat 120, 9052 Zwijnaarde >>> Tel: +32 9 244.66.34 >>> Bioinformatics Training and Services (BITS) >>> http://www.bits.vib.be >>> @bitsatvib >>> >>> On 08/08/2012 12:12 PM, Joachim Jacob wrote: Dear devs, Question about FTP upload: is it correct that Galaxy copies the data from the FTP upload directory to galaxy database instead of symlinking? Can I set somewhere the option to symlink instead of copying? I run galaxy in a small virtual machine. The Galaxy database is on a network share. With 'get data' - 'Upload file', when importing the files I have uploaded with FTP, there is a process filling up the /tmp directory with the file I want to import. Kind regards, Joachim >>> ___ >>> 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/
