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

Tophat issue
by Luciano Cosme 27 Dec '12

27 Dec '12

Howdy, I am getting the following error with tophat: Error in tophat: [2012-12-27 15:08:40] Beginning TopHat run (v2.0.5) ----------------------------------------------- [2012-12-27 15:08:40] Checking for Bowtie Traceback (most recent call last): File "/usr/bin/tophat", line 4035, in <module> sys.exit(main()) File "/usr/bin/tophat", line 3836, in main check_bowtie(params) File "/usr/bin/tophat", line 1473, in check_bowtie bowtie_version = get_bowtie_version(params.bowtie2) File "/usr/bin/tophat", line 1351, in get_bowtie_version bowtie_version = [int(x) for x in ver_numbers[:3]] + [int(ver_numbers[3][4:])] IndexError: list index out of range I tried Tophat and Tophat2 a couple times and always giving me the same error. The reads I am trying to map are from small RNA sequencing project. I am trying to map the unannotated reads back to the genome. I am not sure what is causing this problem, any help will be appreciated. Thank you. Luciano

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Where is the output of tools stored in Galaxy?
by Sachit Adhikari 27 Dec '12

27 Dec '12

Hello Everyone, *Merry Christmas and Happy New Year* * * I was wondering where are the output of the tools stored in the machine where the galaxy is hosted? And, can I change the path of the output of the tools? Thanks, Sachit

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How to refresh the tool panel in Galaxy?
by Huayan Gao 26 Dec '12

26 Dec '12

Hi, I am trying to add a tool into Galaxy. So far everything is ok except that I need to restart the server to make the tool showing up in the tool panel. So my question is that how to refresh the tool panel without restarting the server? After I install a tool from toolshed, I can see the tool immediately from the tool panel. This is exactly the function I want to implement in python. I was reading the code but too complicated. Could you point me the right place(code)? Thanks a lot. Best, Huayan

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Tool reinstall breaking again...
by Franco Caramia 26 Dec '12

26 Dec '12

Hi list, Merry Christmas to all! I installed the "homer" tool from the main galaxy toolshed and then made a pull to revision : 8414:36ad8aa7b922 Then uninstalled the tool and tried to reinstall and got the following error: URL: http://115.146.94.148/admin_toolshed/reselect_tool_panel_section?id=b9a95d0… Module paste.exceptions.errormiddleware:*144* in __call__ >> <http://115.146.94.148/admin_toolshed/reselect_tool_panel_section?id=b9a95d0…> app_iter *=* self*.*application*(*environ*,* sr_checker*)* Module paste.debug.prints:*106* in __call__ >> <http://115.146.94.148/admin_toolshed/reselect_tool_panel_section?id=b9a95d0…> environ*,* self*.*app*)* Module paste.wsgilib:*543* in intercept_output >> <http://115.146.94.148/admin_toolshed/reselect_tool_panel_section?id=b9a95d0…> app_iter *=* application*(*environ*,* replacement_start_response*)* Module paste.recursive:*84* in __call__ >> <http://115.146.94.148/admin_toolshed/reselect_tool_panel_section?id=b9a95d0…> *return* self*.*application*(*environ*,* start_response*)* Module paste.httpexceptions:*633* in __call__ >> <http://115.146.94.148/admin_toolshed/reselect_tool_panel_section?id=b9a95d0…> *return* self*.*application*(*environ*,* start_response*)* Module galaxy.web.framework.base:*160* in __call__ >> <http://115.146.94.148/admin_toolshed/reselect_tool_panel_section?id=b9a95d0…> body *=* method*(* trans*,* ****kwargs *)* Module galaxy.web.framework:*206* in decorator >> <http://115.146.94.148/admin_toolshed/reselect_tool_panel_section?id=b9a95d0…> *return* func*(* self*,* trans*,* ***args*,* ****kwargs *)* Module galaxy.webapps.galaxy.controllers.admin_toolshed:*1445* in reselect_tool_panel_section >> <http://115.146.94.148/admin_toolshed/reselect_tool_panel_section?id=b9a95d0…> response *=* urllib2*.*urlopen*(* url *)* Module urllib2:*126* in urlopen >> <http://115.146.94.148/admin_toolshed/reselect_tool_panel_section?id=b9a95d0…> *return* _opener*.*open*(*url*,* data*,* timeout*)* Module urllib2:*406* in open >> <http://115.146.94.148/admin_toolshed/reselect_tool_panel_section?id=b9a95d0…> response *=* meth*(*req*,* response*)* Module urllib2:*519* in http_response >> <http://115.146.94.148/admin_toolshed/reselect_tool_panel_section?id=b9a95d0…> 'http'*,* request*,* response*,* code*,* msg*,* hdrs*)* Module urllib2:*444* in error >> <http://115.146.94.148/admin_toolshed/reselect_tool_panel_section?id=b9a95d0…> *return* self*.*_call_chain*(****args*)* Module urllib2:*378* in _call_chain >> <http://115.146.94.148/admin_toolshed/reselect_tool_panel_section?id=b9a95d0…> result *=* func*(****args*)* Module urllib2:*527* in http_error_default >> <http://115.146.94.148/admin_toolshed/reselect_tool_panel_section?id=b9a95d0…> *raise* HTTPError*(*req*.*get_full_url*(**)**,* code*,* msg*,* hdrs*,* fp*)* *HTTPError: HTTP Error 404: Not Found* Any ideas on what could be happening?? I did the same before the pull and everything seemed to be working correctly... Thanks, Franco

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Re: [galaxy-dev] installing BWA from toolshed
by Greg Von Kuster 23 Dec '12

23 Dec '12

Hi Quang, I didn't realize you were running on the cloud, which is not my area of expertise - my instructions were for a local Galaxy instance. I'll let others with more knowledge of the cloud environment answer your question. Please keep all replies on the mail list to enable optimal response to questions and issues. Greg Von Kuster On Dec 22, 2012, at 10:45 AM, Quang Trinh wrote: > Hi Greg, > Quick question: I am running off Amazon EC2 and when I do the > upgrade, I get the following error: > > Not trusting file /mnt/galaxyTools/galaxy-central/.hg/hgrc from > untrusted user galaxy, group galaxy > Not trusting file /mnt/galaxyTools/galaxy-central/.hg/hgrc from > untrusted user galaxy, group galaxy > abort: repository default not found! > > How do I get around this? > > THanks, > > On 12/22/12, Quang Trinh <quang.trinh(a)gmail.com> wrote: >> Thanks Greg, will follow the instructions from the news brief. >> >> Q >> >> On Sat, Dec 22, 2012 at 10:14 AM, Greg Von Kuster <greg(a)bx.psu.edu> wrote: >>> Hi Quang, >>> >>> You'll need to upgrade your Galaxy instance to the distribution release >>> that went out on December 20. Here is the link to the news brief for the >>> December 20 release. >>> >>> http://wiki.galaxyproject.org/DevNewsBriefs/2012_12_20 >>> >>> From this point forward, all communication between Galaxy and the tool >>> shed will be backward compatible to this December 20 release, so new tool >>> shed features introduced in the future will function for any Galaxy >>> instance running the December 20 release or newer. >>> >>> Greg Von Kuster >>> >>> >>> On Dec 22, 2012, at 9:53 AM, Quang Trinh wrote: >>> >>>> Hi, >>>> Trying to install BWA from toolshed just now and I get these error >>>> messages ( see below ). Installing BWA from toolshed works for me >>>> before. >>>> >>>> Thanks >>>> >>>> Q >>>> >>>> >>>> Server Error >>>> >>>> URL: >>>> http://54.242.71.44/admin_toolshed/prepare_for_install?tool_shed_url=http:/… >>>> Module paste.exceptions.errormiddleware:143 in __call__ >>>>>> app_iter = self.application(environ, start_response) >>>> Module paste.debug.prints:98 in __call__ >>>>>> environ, self.app) >>>> Module paste.wsgilib:539 in intercept_output >>>>>> app_iter = application(environ, replacement_start_response) >>>> Module paste.recursive:80 in __call__ >>>>>> return self.application(environ, start_response) >>>> Module paste.httpexceptions:632 in __call__ >>>>>> return self.application(environ, start_response) >>>> Module galaxy.web.framework.base:160 in __call__ >>>>>> body = method( trans, **kwargs ) >>>> Module galaxy.web.framework:206 in decorator >>>>>> return func( self, trans, *args, **kwargs ) >>>> Module galaxy.webapps.galaxy.controllers.admin_toolshed:1199 in >>>> prepare_for_install >>>>>> description, repository_clone_url, changeset_revision, ctx_rev, >>>>>> repository_owner, tool_dependencies = repo_info_tuple >>>> ValueError: too many values to unpack >>>> ___________________________________________________________ >>>> 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/ >>> >>

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installing BWA from toolshed
by Quang Trinh 22 Dec '12

22 Dec '12

Hi, Trying to install BWA from toolshed just now and I get these error messages ( see below ). Installing BWA from toolshed works for me before. Thanks Q Server Error URL: http://54.242.71.44/admin_toolshed/prepare_for_install?tool_shed_url=http:/… Module paste.exceptions.errormiddleware:143 in __call__ >> app_iter = self.application(environ, start_response) Module paste.debug.prints:98 in __call__ >> environ, self.app) Module paste.wsgilib:539 in intercept_output >> app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ >> return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ >> return self.application(environ, start_response) Module galaxy.web.framework.base:160 in __call__ >> body = method( trans, **kwargs ) Module galaxy.web.framework:206 in decorator >> return func( self, trans, *args, **kwargs ) Module galaxy.webapps.galaxy.controllers.admin_toolshed:1199 in prepare_for_install >> description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, tool_dependencies = repo_info_tuple ValueError: too many values to unpack

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Galaxy December 20, 2012 Distribution & News Brief
by Jennifer Jackson 22 Dec '12

22 Dec '12

*Galaxy Dec 20, 2012 Distribution & News Brief <http://wiki.galaxyproject.org/News/2012_12_20_DistributionNewsBrief>* *Complete News Brief <http://wiki.galaxyproject.org/DevNewsBriefs/2012_12_20>* *Highlights:* * *Required Metadata Reset* for instances running *Tool Shed <http://wiki.galaxyproject.org/Tool%20Shed>* repositories. Be sure to *learn how <http://wiki.galaxyproject.org/ResettingMetadataForInstalledRepositories>*. * *Simplified tool config*: all tools (including tool shed repos) can now have handlers and runners assigned based on their "short id". * *New* GFF <http://wiki.galaxyproject.org/Learn/Datatypes#GFF>/GFF3 <http://wiki.galaxyproject.org/Learn/Datatypes#GFF3> annotation support for *Cuffcompare/merge/diff <http://cufflinks.cbcb.umd.edu/manual.html>*. * *More Updated* tools: *TopHat2 <http://tophat.cbcb.umd.edu/manual.html>*, *Bowtie2 <http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml>*. * *Multiple pull-requests* contributed by community (thanks!): *#83 <https://bitbucket.org/galaxy/galaxy-central/pull-request/83/allow-a-datatyp…>*, *#85 <https://bitbucket.org/galaxy/galaxy-central/pull-request/85/another-round-o…>*, *#90 <https://bitbucket.org/galaxy/galaxy-central/pull-request/90/patch-to-make-e…>*, *#91* <https://bitbucket.org/galaxy/galaxy-central/pull-request/91/fixing-missing-…>. * *Issue tracking help* is now covered in detailed in our new wiki: *Using the Galaxy Issue Board <http://wiki.galaxyproject.org/Issues>* * *GCC2013 Training Day Topic Nominations <http://wiki.galaxyproject.org/Events/GCC2013/TrainingDay> are now open* through /*January 11th*/ <http://wiki.galaxyproject.org/Events/GCC2013/KeyDates> * *Plus* more *Tool Shed <http://wiki.galaxyproject.org/Tool%20Shed>* updates, *Bug Fixes*, and improvements to *Trackster, UI, Libraries, and Histories*. * getgalaxy.org <http://getgalaxy.org>* *bitbucket.org/galaxy/galaxy-dist <http://bitbucket.org/galaxy/galaxy-dist>* *galaxy-dist.readthedocs.org <http://galaxy-dist.readthedocs.org> * new: $ hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist upgrade: $ hg pull -u -r 36ad8aa7b922 *Best wishes for a safe and happy holiday*, /*The Galaxy Team <http://wiki.galaxyproject.org/Galaxy%20Team>*/ -- Jennifer Jackson http://galaxyproject.org

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Xgrid and Galaxy
by James Boocock 21 Dec '12

21 Dec '12

Hi All, For a summer project I have created a XGRID module when writing the interface I tried to follow the model of the other runners like PBS. I know XGRID is a dead technology but the binaries can be transferred to the new Mac OSX version and is supposed to successfully run on there. I have currently tested it on our galaxy distribution and run some test jobs on the xgrid that has been made available to us over the summer ( its summer here for us in new zealand!). This would only be for mac installation of galaxy as my XGRID interface uses pyxg which uses PyObjc If anyone would like to use galaxy with XGRID or potentially help me test the module I could make a version available for you. If anyone on this list is interested get back to me. Cheers James.

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Tophat2, Bowtie2 and Bowtie returns empty file
by Sachit Adhikari 21 Dec '12

21 Dec '12

Tophat2, Tophat, Bowtie2 returns the empty file. The output is in the format: *Galaxy5-[Bowtie2_on_data_4__mapped_reads]* Whenever I open it by double clicking I get the empty file which 0 bytes file size. I am using hg19 index. What might be the problem?

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GenePeeks is hiring a tools programmer
by Adam Cohn 20 Dec '12

20 Dec '12

Genetics Tools Programmer - Position Description GenePeeks is a unique genetic information company with a mission to help families protect the health of their future children. We are searching for a tools programmer to join our growing team and help develop leading-edge technologies in a fast-paced, early-stage environment. Primary duties: Assist our Science Team by developing automated data retrieval and display tools to assist in genetic data analysis. Will require database queries and accessing online database resources through API. A good grasp of SQL and some experience with Python (or similar programming language) is required. Experience with Genetics, Biology and associated tools (Such as NMCBI and Galaxy) is desirable but not absolutely required. Must be fast working, flexible, and have a sense of humor. The work will start out as part time temporary - could become full time permanent if budget and circumstances allow. General Requirements: - Ability and motivation to work independently - Ability to interact proactively with a small group - Strong written and verbal communication skills - Desire to work in a fast-paced, loosely structured business environment - Sense of humor - -Location:- Cambridge, MA or New York, NY. - Some travel may be required -Contact Information: If you are interested in this role and fulfill the requirements, please send your CV and cover letter to jobs(a)genepeeks.com -- Adam S. Cohn Chief Technology Officer / Chief Operations Officer GenePeeks 175 Varick Street, New York, NY (646) 664-4268 (703) 473-8811 (mobile) adamcohn(a)genepeeks.com www.geenpeeks.com

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