December 2012 - galaxy-dev - lists.galaxyproject.org

Edit login page
by Zinonas Antoniou 05 Dec '12

05 Dec '12

Hello, I need your help. I need to edit the login page of galaxy and show another way of login in our platform, except of simple login and openid options. I want to have another option for external login. Can you help me please, how to do it? Thank you in advance, Zinonas

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from shed to shed
by Ido Tamir 05 Dec '12

05 Dec '12

Hi, how do I get tools from one local toolshed (or the main galaxy toolshed) into another tool-shed? Is it possible to clone the content of a complete tool-shed - all repositories at once into another tool-shed? Can I then import all the tools at once into a local galaxy instance? We have a group with their own tool-shed. Unfortunately, I accessed it directly without a proxy on its port which leads to a problem described in issue 825 in galaxy-central. I want to a) clone the tool-shed as it is into my own tool-shed (rsync?) b) selectively or bulk install these tools into my galaxy server. thank you very much, ido

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Advice on running reports interface in production setting
by Peter Briggs 05 Dec '12

05 Dec '12

Hello The Galaxy reports interface (run_reports.sh) looks immensely useful for getting a handle on the usage of our local Galaxy, and I was wondering if anyone could offer advice on how they run the reports in a production environment. In terms of setting up and running the reports server, there doesn't appear to be much documentation however the instructions in the June 8th 2010 news brief covers the basics adequately: http://wiki.galaxyproject.org/DevNewsBriefs/2010%2006_08?highlight=%28repor… This looks okay for running in an ad-hoc fashion (i.e. start it up, look at the reports in a browser running on localhost, shut it down again as required) but does anyone run it in a more persistent set-up? Or is ad-hoc the way to go? Any suggestions welcome, many thanks Best wishes, Peter -- Peter Briggs peter.briggs(a)manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482

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(no subject)
by Игорь Заигрин 05 Dec '12

05 Dec '12

Hi, Is it possible to display different content of central area (welcome.html) according to user - registered or guest? If guest - page with offer to register, if registered user - page with another info. And how I can get the email of this user? Thanks for your help! Igor.

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Key error in latest build of galaxy-central
by Anthonius deBoer 04 Dec '12

04 Dec '12

Got this when trying to install GMAP from the tool shed... Any ideas? Error Traceback: View as: Interactive | Text | XML (full) ⇝ KeyError: 'includes_repository_dependencies' URL: http://srv151/admin_toolshed/prepare_for_install?tool_shed_url=http://tools… Module weberror.evalexception.middleware:364 in respond view >> app_iter = self.application(environ, detect_start_response) Module paste.debug.prints:98 in __call__ view >> environ, self.app) Module paste.wsgilib:539 in intercept_output view >> app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ view >> return self.application(environ, start_response) Module galaxy.web.framework.middleware.remoteuser:91 in __call__ view >> return self.app( environ, start_response ) Module paste.httpexceptions:632 in __call__ view >> return self.application(environ, start_response) Module galaxy.web.framework.base:160 in __call__ view >> body = method( trans, **kwargs ) Module galaxy.web.framework:206 in decorator view >> return func( self, trans, *args, **kwargs ) Module galaxy.webapps.galaxy.controllers.admin_toolshed:1070 in prepare_for_install view >> includes_repository_dependencies = util.string_as_bool( repo_information_dict[ 'includes_repository_dependencies' ] ) KeyError: 'includes_repository_dependencies'

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Running galaxy on multiple, physical servers
by Anthonius deBoer 04 Dec '12

04 Dec '12

Hi, I am trying to figure out how to run galaxy distributed over several physical servers, with different IP addresses... The wiki on scaling and load balancing only speaks of balancing on the same physical server, but does not address how to put a handful of managers on a different physical server... Any ideas how to do this? I guess I can just copy the .ini file, define managers in that and try to start it on that server, but I am hesitant until I know this can work at all... Thanks http://wiki.galaxyproject.org/Admin/Config/Performance/Web%20Application%20… Thon

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Can't find new pause / resume functionality in Dec 2012 Galaxy
by Greg Edwards 04 Dec '12

04 Dec '12

Hi all, I was keen to try the new Pause / Resume functionality mentuioned in http://wiki.galaxyproject.org/News/2012_12_03_DistributionNewsBrief but can't see it anywhere, in Galaxy or searches. It's not on the Test site at https://test.g2.bx.psu.edu/ or production at https://main.g2.bx.psu.edu/ Can you point me to where I can try it ? Thanks, -- Greg Edwards, Port Jackson Bioinformatics gedwards2(a)gmail.com

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Required Galaxy umask settings for HTML downloads?
by Josh Nielsen 04 Dec '12

04 Dec '12

Hello all, I am having issues downloading HTML files from Galaxy the same as is described in this email chain: http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-August/010965.html I am getting the error "(13)Permission denied: xsendfile: cannot open file: /basedir/galaxy_data/database/tmp/tmp8iEccn/library_download.zip" which is indeed a basic filesystem permissions issue. The problem is that the permissions created for that directory and every directory created in tmp/ look like this: drwx------+ 2 galaxy galaxy 3 Dec 4 09:23 tmp8iEccn And I have placed the Apache user in the galaxy group, but as you can see no group permissions ever get set by Galaxy on the directories that it creates (it is getting a 700 permissions setting). As Nate Coraor suggested in the message linked to above, I have tried altering the default umask but I ran into issues with getting non-existant results. I use "sudo service galaxy start" as the galaxy user each time to start the server and a "ps -ef | grep galaxy" confirms that Galaxy is running as the galaxy user. Since I use sudo though I changed the sudoers file to include: root ALL=(ALL) ALL galaxy ALL=(ALL) ALL Defaults umask_override Defaults umask = 0002 This changed absolutely nothing. Then I started looking deeper into the PAM configuration and added a umask directive to /etc/pam.d/sudo (and also tried it in password-auth-ac and system-auth-ac) like this: "session optional pam_umask.so umask=0002". Still nothing changed in the permissions in tmp/ when I tried to download an HTML file: no group permissions were set. Then I dug deeper still and saw that sometimes if setting the mask in /etc/pam.d/ config files is not enough that you can try to set a system-wide mask in /etc/login.defs (following the suggestion here: http://stackoverflow.com/questions/10220531/how-to-set-system-wide-umask) Still no dice. I've pretty much exhausted my know-how in this department. Any other suggestions of how to fix this or where the correct place to set the umask is? Thanks, Josh Nielsen

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Re: [galaxy-dev] Speed up the galaxy
by Ido Tamir 04 Dec '12

04 Dec '12

> Hi all, > > How can I speed up the galaxy? Like how to use more cores and memeries. http://wiki.galaxyproject.org/Admin/Config/Performance/Production%20Server http://wiki.galaxyproject.org/Admin/Config/Performance/Web%20Application%20… HTH, ido

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Same error, better formatting.
by Franco Caramia 04 Dec '12

04 Dec '12

URL: http://bioinf-galaxy/admin_toolshed/browse_repositories?operation=activate+… Module paste.exceptions.errormiddleware:*143* in __call__ >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa…> app_iter *=* self*.*application*(*environ*,* start_response*)* Module paste.debug.prints:*98* in __call__ >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa…> environ*,* self*.*app*)* Module paste.wsgilib:*539* in intercept_output >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa…> app_iter *=* application*(*environ*,* replacement_start_response*)* Module paste.recursive:*80* in __call__ >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa…> *return* self*.*application*(*environ*,* start_response*)* Module paste.httpexceptions:*632* in __call__ >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa…> *return* self*.*application*(*environ*,* start_response*)* Module galaxy.web.framework.base:*160* in __call__ >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa…> body *=* method*(* trans*,* ****kwargs *)* Module galaxy.web.framework:*184* in decorator >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa…> *return* func*(* self*,* trans*,* ***args*,* ****kwargs *)* Module galaxy.web.controllers.admin_toolshed:*350* in browse_repositories >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa…> *return* self*.*reselect_tool_panel_section*(* trans*,* ****kwd *)* Module galaxy.web.framework:*184* in decorator >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa…> *return* func*(* self*,* trans*,* ***args*,* ****kwargs *)* Module galaxy.web.controllers.admin_toolshed:*1352* in reselect_tool_panel_section >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa…> status*=*status *)* Module galaxy.web.framework:*746* in fill_template >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa…> *return* self*.*fill_template_mako*(* filename*,* ****kwargs *)* Module galaxy.web.framework:*757* in fill_template_mako >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa…> *return* template*.*render*(* ****data *)* Module mako.template:*296* in render >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa…> *return* runtime*.*_render*(*self*,* self*.*callable_*,* args*,* data*)* Module mako.runtime:*660* in _render >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa…> ****_kwargs_for_callable*(*callable_*,* data*)**)* Module mako.runtime:*692* in _render_context >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa…> _exec_template*(*inherit*,* lclcontext*,* args*=*args*,* kwargs*=*kwargs*)* Module mako.runtime:*718* in _exec_template >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa…> callable_*(*context*,* ***args*,* ****kwargs*)* Module _base_mako:*42* in render_body >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa…> __M_writer*(*unicode*(*next*.*body*(**)**)**)* Module _admin_tool_shed_repository_reselect_tool_panel_section_mako:*76* in render_body >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa…> __M_writer*(*unicode*(*render_tool_dependency_section*(* install_tool_dependencies_check_box*,* *[* repo_info_dict *]* *)**)**)* Module _admin_tool_shed_repository_common_mako:*204* in render_render_tool_dependency_section >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa…> changeset_revision *)* Module posixpath:*67* in join >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa…> *elif* path *==* '' *or* path*.*endswith*(*'/'*)**:* *AttributeError: 'NoneType' object has no attribute 'endswith'*

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