galaxy-dev August 2013

galaxy-dev@lists.galaxyproject.org

116 participants
210 discussions

Re: [galaxy-dev] Running local galaxy installation while another httpd is operating on the same computer
by Nate Coraor 06 Aug '13

06 Aug '13

On Aug 5, 2013, at 12:33 PM, Boaz Shaanan wrote: > Hi, > > I think I'm running into a problem of getting my local galaxy installation server to start because another httpd server is currently running on the same computer (see attached output of run.sh). Toward the end I notice that the server starts with PID number but then runs into a socket conflict (probably with the other server) and stops. Is there a way to get over this problem? > > Thanks for your help. > > Boaz Hi Boaz, If you're starting on a port other than 80 and intend to just access that port directly or via a proxy server, you can change the port number at the top of universe_wsgi.ini. If you're trying to start Galaxy on port 80, you'll have to decide which application you want to give that privilege to, since it can't be more than one. However, a common and recommended solution to this problem is to run a proxy server on port 80. Instructions on how to place Galaxy behind a proxy server are available at: http://usegalaxy.org/production --nate > > > Boaz Shaanan, Ph.D. > Dept. of Life Sciences > Ben-Gurion University of the Negev > Beer-Sheva 84105 > Israel > > E-mail: bshaanan(a)bgu.ac.il > Phone: 972-8-647-2220 Skype: boaz.shaanan > Fax: 972-8-647-2992 or 972-8-646-1710 > > > > > <run.sh.out>___________________________________________________________ > 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/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/

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Invalid Galaxy URL: None - Installing Tools Shed
by Adam Brenner 06 Aug '13

06 Aug '13

Howdy, I am trying to install a tools shed item, Emboss, but when I do this via the admin interface, I get the following text: Repository installation is not possible due to an invalid Galaxy URL: None. You may need to enable cookies in your browser. I have searched the universe_wsgi.ini file and could not find anything that looks like Galaxy URL. Any ideas on how to set the Galaxy URL? Thanks, -Adam -- Adam Brenner Computer Science, Undergraduate Student Donald Bren School of Information and Computer Sciences Research Computing Support Office of Information Technology http://www.oit.uci.edu/rcs/ University of California, Irvine www.ics.uci.edu/~aebrenne/ aebrenne(a)uci.edu

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datatype logic
by Ted Goldstein, Ph.D. 06 Aug '13

06 Aug '13

If I share a history, it produces a url with the datasets. This is good. But if you click on the eyeball in this view, it shows the dataset in its raw form. Its as if the code path does not go through the sophisticated datatype logic. Is this deliberate or an oversight? Thanks, Ted

2 1

How to Uninstall NCBI_Blast_Plus from ToolShed
by Rodolfo Aramayo 06 Aug '13

06 Aug '13

People, I successfully installed NCBI_Blast_Plus from the toolshed The tool, however, failed to work giving the following error: Fatal error: Exit code 255 () Error: NCBI C++ Exception: "/usr/local/galaxy/galaxy-dist/database/tmp/tmpwL5OFq/ncbi-blast-2.2.26+-src/c++/src/corelib/ncbiobj.cpp", line 689: Critical: ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL pointer. I then tried uninstalling/reinstalling the tool However I now get an eternal 'installing' grey message and when I click 'manage the repo' I get: ######### URL: http://galaxy.tamu.edu/admin_toolshed/manage_repository?id=ff08d6222f8e1499… File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 221 in decorator return func( self, trans, *args, **kwargs ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 561 in manage_repository repository = suc.get_installed_tool_shed_repository( trans, repository_id ) File '/usr/local/galaxy/galaxy-dist/lib/tool_shed/util/shed_util_common.py', line 515 in get_installed_tool_shed_repository return trans.sa_session.query( trans.model.ToolShedRepository ).get( trans.security.decode_id( id ) ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/security/__init__.py', line 60 in decode_id return int( self.id_cipher.decrypt( obj_id.decode( 'hex' ) ).lstrip( "!" ) ) ValueError: invalid literal for int() with base 10: 'cb73864b36ce6a1b' ######### How can I totally uninstall and re-install this tool? Thanks

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Re: [galaxy-dev] Running local galaxy installation while another httpd is operating on the same computer
by Dannon Baker 05 Aug '13

05 Aug '13

Hi Boaz, You should be able to edit universe_wsgi.ini (line ~30) to specify any port you'd like -- so simply pick something other than 8080, save the file, and retry. Remember to remove the hash (#) at the beginning of the line to have it take effect. -Dannon On Mon, Aug 5, 2013 at 12:42 PM, Boaz Shaanan <bshaanan(a)bgu.ac.il> wrote: > Hi, > > I think I'm running into a problem of getting my local galaxy > installation server to start because another httpd server is currently > running on the same computer (see attached output of run.sh). Toward the > end of the attached file you'll notice that the server starts with PID > number but then runs into a socket conflict (probably with the other > server) and stops. Is there a way to get over this problem? Or am I wrong > in my diagnosis? > > I did manage to get the galaxy server to start about 2 weeks ago while > no other httpd server was running. I then switched the galaxy server off > and now I run into this problem while trying to restart it. > > Thanks for your help. > > Boaz > > > > *Boaz Shaanan, Ph.D. > Dept. of Life Sciences > Ben-Gurion University of the Negev > Beer-Sheva 84105 > Israel > > E-mail: bshaanan(a)bgu.ac.il > Phone: 972-8-647-2220 Skype: boaz.shaanan > Fax: 972-8-647-2992 or 972-8-646-1710 * > ** > ** > * > > * > > ___________________________________________________________ > 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/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ >

2 1

2014 Galaxy Training Survey
by Dave Clements 05 Aug '13

05 Aug '13

Hello all, The Galaxy Project is asking for your help on how we should focus our training efforts for the coming year. If you are interested in Galaxy Training, please take a few minutes to let us know what you would like to see offered, and where you would like training to be held: http://bit.ly/gxy14training Thanks in advance for your time and input, Dave C -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

1 0

lessc compiler error on blue_colors.ini
by Seth Sims 05 Aug '13

05 Aug '13

Dear Galaxy devs, I am attempting to create a style directory to match my school's look and feel. I am mainly trying to get the development environment setup to do this right now. My current problem is that when I attempt to compile the standard blue_colors.ini which comes with galaxy I am receiving a syntax error: ParseError: Syntax Error on line 1 in /srv/galaxy-dist/static/style/blue_colors.ini:1:10 1 base_text=#303030 2 base_bg_top=#FFFFFF I have not edited that file at all. So the first question is, what version of lessc is being used to compile the styles for the basic installation? Also are there any pitfalls I should be aware of with this process. - Seth

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Problems with running jobs on Galaxy
by Philipp Kapranov 05 Aug '13

05 Aug '13

Hello, I have submitted some simple jobs to Galaxy Main last Friday and they are still waiting to be run. Are there any issues with the cluster? Thank you, Phil Philipp Kapranov, PhD

1 0

History & Visualization list empty
by Benjamin Schuster-Boeckler 05 Aug '13

05 Aug '13

Hi there, I've set up a local galaxy installation that so far is working very nicely. However one little issue that I'm having is that the "Saved Visualizations" and "Saved Histories" lists are empty, even though I have multiple histories and multiple visualizations. In fact, when I choose to visualize a dataset in Trackster and select "View in saved visualization", I DO see the list of existing visualizations. Pictures attached. The identical problem appears with Histories. Any idea what the problem might be? I tried in Chrome and Safari, I logged out and back in, I restarted the server, but nothing fixed the issue... Thanks in advance for the help, Ben -- Benjamin Schuster-Böckler Leadership Fellow for Bioinformatics Ludwig Institute for Cancer Research University of Oxford Old Road Campus Research Building Oxford OX3 7DQ United Kingdom [cid:CD86F63E-0203-45D3-8802-328573CCB3B1][cid:BECC9A41-D145-4D11-A38A-485DAAB3997E]

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Galaxy jobs running on cluster can't stop.
by shenwiyn 05 Aug '13

05 Aug '13

Hi everyone, I run my galaxy jobs of Megablast on cluster ,but when I want to kill my Megablast by clicking , the job keeps on running in my background.The job_conf.xml I set as follows: <destination id="long_jobs" runner="pbs" tags="cluster"> <param id="Resource_List">walltime=72:00:00,nodes=2:ppn=8,mem=16G</param> <param id="galaxy_external_runjob_script">scripts/drmaa_external_runner.py</param> <param id="galaxy_external_killjob_script">scripts/drmaa_external_killer.py</param> <param id="galaxy_external_chown_script">scripts/external_chown_script.py</param> </destination> <tools> <tool id="megablast_wrapper" destination="long_jobs"/> </tools> Could anyone give me some help please?Thank you. shenwiyn

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galaxy-dev August 2013