June 2013 - galaxy-dev - lists.galaxyproject.org

API updating meta data for a history
by Philip Mabon 20 Jun '13

20 Jun '13

Hey, I was curious if it was possible to allow the API to change tags associated with a history? At the moment in the galaxy code it's forbidden. Having the ability to add tags using the API would be helpful of associating multiple histories to a particular project. So later, it would be easier to 'select' all the histories to perform a bulk action. Ie download all contigs.fasta from histories that tag with 'project_Ecoli_June20_2013'. Thanks Phil

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retrieving file info from '.dat' dataset
by vijayalakshmi 20 Jun '13

20 Jun '13

Hi all, I have written a java tool to which I have to pass an existing file's name. In the XML wrapper, I am choosing the file from the history using <param type="data">. Even though the tool is receiving the filename as an input, it is looking for a ".dat" file from \database\000\<some dataset> How do I retrieve the file I need from the dataset? Thanks, VJ.

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Re: [galaxy-dev] simplest way to connect RNAseq tools for a local Galaxy instance
by Nicholas Kline 20 Jun '13

20 Jun '13

Hi Elwood, I am in a similar situation. Our lab is trying to connect Bowtie version 1 to our local Galaxy framework. We are slowly making progress with the help of people at seqanswers.com You are welcome to review the thread I started at http://seqanswers.com/forums/showthread.php?t=31047 since it might contain information that relates to your situation. If you do not receive help from this mailing list, I recommend posting your question at seqanswers.com Good luck! > Message: 22 > Date: Thu, 20 Jun 2013 11:45:20 -0400 > From: Elwood Linney <ellinney(a)gmail.com> > To: galaxy-dev(a)lists.bx.psu.edu > Subject: [galaxy-dev] simplest way to connect RNAseq tools for a local > Galaxy instance > Message-ID: > <CAC-Zp0yDhx5Dr0ffdtRB-h=uLZR5UZaBkyVh+8riFYemNmwVnw(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > I have: > 1) downloaded the Galaxy framework into a Mac Pro desktop with 64gb ram > 2) downloaded Mac OS versions of Tophat2, Bowtie2, and the Cufflink suite > to the mac > 3) have looked at the Galaxy wiki on connecting these > [http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies] > 4) I have gotten some useful advice from Dannon Baker on how to introduce > my large datasets on the some computer into Galaxy through Admin changing > some permissions > > but my minimal knowledge of unix commands and tricks has me stymied > > Question: > If my primary purpose is to use this local instance for the analysis of > RNAseq data within my lab, what is the simplest way of connecting the > programs to the Galaxy framework? > > While from reviewing info on the Galaxy website I am only guessing that > adding them to $PATH might be the easiest way for me to do this (but I am > not exactly sure what this means or specifically how I would do it in my > case). However, I do initiate the running of Galaxy by sh run.sh on my > terminal and visualizing things via my localhost port. There is some > indication from the wiki I found that this might not be good for a system > initiated by sh run.sh . > > [http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies] under > "Local Jobs" > > I would appreciate any specific advice on this. > > Sincerely, > > Elwood Linney > DUMC >

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Default history
by Jordi Vaquero 20 Jun '13

20 Jun '13

Hello everyone, I am managing an instance of galaxy. We want to provide a set of example datasets for being used, we want this is by default datasets accessible for the anonymous user. there is any way to do that? I have tried to work the shared and publish option of history but they don't work as I wanted. Thank you in advanced Jordi

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Developing Tools
by Saliya Ekanayake 20 Jun '13

20 Jun '13

Hi, I am new to development with Galaxy and wonder if someone could kindly help me out with the following. 1.) A step-by-step guide on how to develop a tool 2.) Are tools limited to simple functions that run on a single node? 3.) When Galaxy is run on cloud (with EC2) how does it utilize worker nodes? Is it such that steps in my workflow get load balanced into nodes? Thank you, Saliya -- Saliya Ekanayake esaliya(a)gmail.com Cell 812-391-4914 Home 812-961-6383 http://saliya.org

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Re: [galaxy-dev] Messed up a tool installation from a local toolshed
by Greg Von Kuster 20 Jun '13

20 Jun '13

Hello Joachim, It looks like you have an invalid URL you are attempting to us for your top shed (this looks to me like your Galaxy paster log, not your tool shed paster log). Is your tool shed running at 'http://localhost:9009/, or some other port? Also, when this error occurs, you can point your browser to the link displayed in the log where it states "Debug at: http://localhost/_debug/view/1371632354", and it should display a traceback which should help determine issues like this. Greg Von Kuster On Jun 20, 2013, at 4:39 AM, Joachim Jacob | VIB | <joachim.jacob(a)vib.be> wrote: > Hello Greg, > > The version of Galaxy: > arent: 9944:cea3ddf6cdda tip > Update tag for stable_2013.06.03 > branch: stable > > Sorry, forgot to paste the web.log: > ***************************** > tool_shed.tool_shed_registry DEBUG 2013-06-20 10:35:45,718 Invalid url 'http://localhost:9009/' received by tool shed registry's password_manager_for_url method. > ::1 - - [20/Jun/2013:10:35:45 +0200] "GET /admin_toolshed/prepare_for_install?tool_shed_url=http://localhost:9009/&repository_ids=84cbaf0b6bf7a1a9&changeset_revisions=fc2339abcab7 HTTP/1.1" 500 - "http://localhost/admin_toolshed/browse_repositories" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.31 (KHTML, like Gecko) Chrome/26.0.1410.63 Safari/537.31" > Debug at: http://localhost/_debug/view/1371632354 > ***************************** > > Cheers, > Joachim > > Joachim Jacob > Contact details: http://www.bits.vib.be/index.php/about/80-team > > > On 06/20/2013 01:07 AM, Greg Von Kuster wrote: >> Hello Joachim, >> >> What version of Galaxy are you running? >> >> It looks like the 500 error should be displayed in your tool shed's paster log. >> >> Thanks, >> >> Greg Von Kuster >> >> >> On Jun 19, 2013, at 2:46 AM, Joachim Jacob | VIB | <joachim.jacob(a)vib.be> wrote: >> >>> Hi Greg, >>> >>> Thanks, and sorry for the long delay in response. >>> >>> To make the problem clear: https://dl.dropboxusercontent.com/u/18352887/GalaxyToolShedToolError.ogv >>> >>> The version of our Galaxy is: >>> ***************************** >>> [galaxy@galaxy galaxy-dist]$ hg summary >>> parent: 9944:cea3ddf6cdda tip >>> Update tag for stable_2013.06.03 >>> branch: stable >>> commit: 6 modified, 284 unknown >>> update: (current) >>> ***************************** >>> >>> The logs on the 500 error page is: >>> ***************************** >>> Error Traceback: >>> View as: Interactive | Text | XML (full) >>> â‡ HTTPError: HTTP Error 500: Internal Server Error >>> URL: http://localhost/admin_toolshed/prepare_for_install?tool_shed_url=http://lo… >>> Module weberror.evalexception.middleware:364 in respond view >>>>> app_iter = self.application(environ, detect_start_response) >>> Module paste.recursive:84 in __call__ view >>>>> return self.application(environ, start_response) >>> Module paste.httpexceptions:633 in __call__ view >>>>> return self.application(environ, start_response) >>> Module galaxy.web.framework.base:132 in __call__ view >>>>> return self.handle_request( environ, start_response ) >>> Module galaxy.web.framework.base:190 in handle_request view >>>>> body = method( trans, **kwargs ) >>> Module galaxy.web.framework:221 in decorator view >>>>> return func( self, trans, *args, **kwargs ) >>> Module galaxy.webapps.galaxy.controllers.admin_toolshed:825 in prepare_for_install view >>>>> raw_text = common_util.tool_shed_get( trans.app, tool_shed_url, url ) >>> Module tool_shed.util.common_util:110 in tool_shed_get view >>>>> response = urlopener.open( uri ) >>> Module urllib2:397 in open view >>>>> response = meth(req, response) >>> Module urllib2:510 in http_response view >>>>> 'http', request, response, code, msg, hdrs) >>> Module urllib2:435 in error view >>>>> return self._call_chain(*args) >>> Module urllib2:369 in _call_chain view >>>>> result = func(*args) >>> Module urllib2:518 in http_error_default view >>>>> raise HTTPError(req.get_full_url(), code, msg, hdrs, fp) >>> HTTPError: HTTP Error 500: Internal Server Error >>> ***************************** >>> >>> In the galaxy database, the tool_shed_repository table shows: >>> >>> ******************************** >>> galaxydb=> select id, tool_shed, name, owner, installed_changeset_revision, status, error_message from tool_shed_repository; >>> id | tool_shed | name | owner | installed_changeset_revision | status | error_message >>> ----+------------------------+----------------------------+---------------+------------------------------+-------------+--------------- >>> 4 | toolshed.g2.bx.psu.edu | freebayes | devteam | 213a3d6b579a | Installed | >>> 2 | 192.168.10.23:9009 | glinechart | joachim | 75ef0fbe189a | Installed | >>> 8 | toolshed.g2.bx.psu.edu | bedtools | aaronquinlan | 41bba3e648d1 | Installed | >>> 1 | 192.168.10.24:9009 | quarc_read_quality_control | joachim | fa5ddf4118c0 | Uninstalled | >>> 6 | 192.168.10.23:9009 | fastqseqlen | joachim | 3f22736718ef | Installed | >>> 3 | 192.168.10.23:9009 | quarc_bq | joachim | 4dbdbb424a67 | Installed | >>> 15 | 192.168.10.23:9009 | qualimap_suite | joachim | 8c7e29fa58b5 | Installed | >>> 7 | toolshed.g2.bx.psu.edu | bwa_wrappers | devteam | ffa8aaa14f7c | Installed | >>> 9 | toolshed.g2.bx.psu.edu | picard | devteam | e0232cbac965 | Installed | >>> 11 | toolshed.g2.bx.psu.edu | bowtie_color_wrappers | devteam | fd0914e451c5 | Installed | >>> 12 | toolshed.g2.bx.psu.edu | lastz | devteam | 0801f8207d30 | Installed | >>> 20 | toolshed.g2.bx.psu.edu | htseq_count | lparsons | 62a1de8c8aae | Installed | >>> 21 | toolshed.g2.bx.psu.edu | emboss_datatypes | devteam | a89163f31369 | Installed | >>> 23 | toolshed.g2.bx.psu.edu | trinityrnaseq | bhaas | 177bb1b443db | Installed | >>> 14 | toolshed.g2.bx.psu.edu | fastq_mcf | jjohnson | 217aedbdd0d0 | Installed | >>> 22 | toolshed.g2.bx.psu.edu | emboss_5 | devteam | b45f604a08ac | Installed | >>> 5 | toolshed.g2.bx.psu.edu | deseq_and_sam2counts | nikhil-joshi | 3348f484c49c | Installed | >>> 18 | toolshed.g2.bx.psu.edu | gmap | jjohnson | 93911bac43da | Installed | >>> 19 | toolshed.g2.bx.psu.edu | htseq_count | lparsons | f320093f1e8e | Deactivated | >>> 17 | toolshed.g2.bx.psu.edu | gmap | jjohnson | 6adc485b6dc0 | Uninstalled | >>> 10 | toolshed.g2.bx.psu.edu | bowtie_wrappers | devteam | 0c7e4eadfb3c | Installed | >>> 16 | toolshed.g2.bx.psu.edu | cummerbund | jjohnson | ebb9a992508d | Installed | >>> 24 | toolshed.g2.bx.psu.edu | seq_select_by_id | peterjc | 28d52478ace9 | Installed | >>> 13 | toolshed.g2.bx.psu.edu | lastz_paired_reads | devteam | 96825cee5c25 | Installed | >>> 25 | toolshed.g2.bx.psu.edu | muscle | edward-kirton | 38a28f5f9449 | Installed | >>> 26 | localhost:9009 | hmmer | joachim | fc2339abcab7 | New | >>> 27 | localhost:9009 | hmmer | joachim | d724499758f9 | Uninstalled | >>> 28 | localhost:9009 | blat | joachim | e2b0a830c892 | Installed | >>> 29 | toolshed.g2.bx.psu.edu | prop_venn | idot | cc6707a1e044 | Uninstalled | >>> ***************************** >>> >>> Thanks, >>> >>> Joachim Jacob >>> >>> >>> >>> Van: "Greg Von Kuster" <greg(a)bx.psu.edu <mailto:greg@bx.psu.edu>> >>> Datum: 14-jun.-2013 16:15 >>> Onderwerp: Re: [galaxy-dev] Messed up a tool installation from a local toolshed >>> Aan: "Joachim Jacob" <joachim.jacob(a)gmail.com <mailto:joachim.jacob@gmail.com>> >>> Cc: <galaxy-dev(a)bx.psu.edu <mailto:galaxy-dev@bx.psu.edu>> >>> >>> Hello Joachim, >>> >>> What version of Galaxy are your running? >>> >>> What does the tool shed paster go show for the 500 Internal Server Error? >>> >>> Also, run the following sql manually in your Galaxy database and send the results. >>> >>> select id, tool_shed, name, owner, installed_changeset_revision, status, error_message from tool_shed_repository; >>> >>> Thanks, >>> >>> Greg Von Kuster >>> >>> Joachim Jacob >>> Contact details: http://www.bits.vib.be/index.php/about/80-team >>> >>> >>> On 06/14/2013 09:38 AM, Joachim Jacob | VIB | wrote: >>>> Hi all, >>>> >>>> I have developed a tool in our local Galaxy, and imported it in a local toolshed. I next removed the 'dev' version of the tool in Galaxy, and installed it now via het Tool Shed Manager. >>>> >>>> I got an error that the dependencies could not be installed. If figured it out that it (needed to add an extra shell_command in the tool_dependencies) (and the mount point on my system needs to have exec permissions of course). >>>> >>>> So I updated the tool in the toolshed. BUT, then I uninstalled the tool from Galaxy, and reinstalled it from the Tool Shed ... instead of just updating. Anyway, it has happened. >>>> >>>> Now I have the tool listed in my 'Install Tool Shed Repositories', and when I click on it, it says 'this tool is not installed'. The only action I can apply on this installed tool shed repository is 'Install'. Clicking on that 'install' button, leads me to an error page (http error 500). >>>> >>>> ****************************** >>>> URL: http://localhost/admin_toolshed/prepare_for_install?tool_shed_url=http://lo… >>>> Module weberror.evalexception.middleware:364 in respond view >>>>>> app_iter = self.application(environ, detect_start_response) >>>> Module paste.recursive:84 in __call__ view >>>>>> return self.application(environ, start_response) >>>> Module paste.httpexceptions:633 in __call__ view >>>>>> return self.application(environ, start_response) >>>> Module galaxy.web.framework.base:132 in __call__ view >>>>>> return self.handle_request( environ, start_response ) >>>> Module galaxy.web.framework.base:190 in handle_request view >>>>>> body = method( trans, **kwargs ) >>>> Module galaxy.web.framework:221 in decorator view >>>>>> return func( self, trans, *args, **kwargs ) >>>> Module galaxy.webapps.galaxy.controllers.admin_toolshed:825 in prepare_for_install view >>>>>> raw_text = common_util.tool_shed_get( trans.app, tool_shed_url, url ) >>>> Module tool_shed.util.common_util:110 in tool_shed_get view >>>>>> response = urlopener.open( uri ) >>>> Module urllib2:397 in open view >>>>>> response = meth(req, response) >>>> Module urllib2:510 in http_response view >>>>>> 'http', request, response, code, msg, hdrs) >>>> Module urllib2:435 in error view >>>>>> return self._call_chain(*args) >>>> Module urllib2:369 in _call_chain view >>>>>> result = func(*args) >>>> Module urllib2:518 in http_error_default view >>>>>> raise HTTPError(req.get_full_url(), code, msg, hdrs, fp) >>>> HTTPError: HTTP Error 500: Internal Server Error >>>> ************************************ >>>> >>>> The same happens when I go to the Tool Shed, and try to install the tool from there: Galaxy detects that the tool has been installed before, and points me to that 500 error page. >>>> >>>> Any help is heartily appreciated, >>>> >>>> Thanks, >>>> 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/ >>> >>> To search Galaxy mailing lists use the unified search at: >>> http://galaxyproject.org/search/mailinglists/ >>> >> >> >

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History inconsistency between multiple tabs
by Björn Grüning 20 Jun '13

20 Jun '13

Hi, with the new frameless layout we have found a regression that makes it impossible to work with different histories at the same time. Steps to reproduce: - Open History A, uploading some datasets, doing some calculations, reload one tool - Open Histpry B in a second tab - Go back to History A and click execute, the HDA will be included in History B, not in History A Trello card: https://trello.com/c/UrduzUS0 Thanks, Björn

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proftpd setting
by Petr Novak 20 Jun '13

20 Jun '13

Hi Eveybody, We have notice the problem with logging on our galaxy ftpserver after galaxy server upgrade. The only users who created new account or modified password have the problem with logging to ftp. I have found out that this is caused by modified password hashing. Now galaxy uses PBKDF2 scheme while previously SHA1 hashing was used. This change must be reflected in proftpd configuration. I think that current suggested proftpd configuration (http://wiki.galaxyproject.org/Admin/Config/Upload%20via%20FTP) will not work with new password hash. Can you modify your galaxy wiki to reflect this change? thanks Petr Novak

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Messed up a tool installation from a local toolshed
by Joachim Jacob | VIB | 19 Jun '13

19 Jun '13

Hi all, I have developed a tool in our local Galaxy, and imported it in a local toolshed. I next removed the 'dev' version of the tool in Galaxy, and installed it now via het Tool Shed Manager. I got an error that the dependencies could not be installed. If figured it out that it (needed to add an extra shell_command in the tool_dependencies) (and the mount point on my system needs to have exec permissions of course). So I updated the tool in the toolshed. BUT, then I uninstalled the tool from Galaxy, and reinstalled it from the Tool Shed ... instead of just updating. Anyway, it has happened. Now I have the tool listed in my 'Install Tool Shed Repositories', and when I click on it, it says 'this tool is not installed'. The only action I can apply on this installed tool shed repository is 'Install'. Clicking on that 'install' button, leads me to an error page (http error 500). ****************************** URL: http://localhost/admin_toolshed/prepare_for_install?tool_shed_url=http://lo… Module weberror.evalexception.middleware:364 in respond view >> app_iter = self.application(environ, detect_start_response) Module paste.recursive:84 in __call__ view >> return self.application(environ, start_response) Module paste.httpexceptions:633 in __call__ view >> return self.application(environ, start_response) Module galaxy.web.framework.base:132 in __call__ view >> return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:190 in handle_request view >> body = method( trans, **kwargs ) Module galaxy.web.framework:221 in decorator view >> return func( self, trans, *args, **kwargs ) Module galaxy.webapps.galaxy.controllers.admin_toolshed:825 in prepare_for_install view >> raw_text = common_util.tool_shed_get( trans.app, tool_shed_url, url ) Module tool_shed.util.common_util:110 in tool_shed_get view >> response = urlopener.open( uri ) Module urllib2:397 in open view >> response = meth(req, response) Module urllib2:510 in http_response view >> 'http', request, response, code, msg, hdrs) Module urllib2:435 in error view >> return self._call_chain(*args) Module urllib2:369 in _call_chain view >> result = func(*args) Module urllib2:518 in http_error_default view >> raise HTTPError(req.get_full_url(), code, msg, hdrs, fp) HTTPError: HTTP Error 500: Internal Server Error ************************************ The same happens when I go to the Tool Shed, and try to install the tool from there: Galaxy detects that the tool has been installed before, and points me to that 500 error page. Any help is heartily appreciated, Thanks, Joachim -- Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team

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Possible bug in managing tool shed repositories
by Joachim Jacob | VIB | 19 Jun '13

19 Jun '13

Hi all, Before posting on Trello, perhaps someone can confirm that it is a bug: 1. In the admin menu, go to 'Manage installed tool shed repositories' 2. click on a tool that you have installed with dependencies (!) 3. In the top right 'repository actions', choose 'Manage tool dependencies' 4. In the top right 'Actions', choose 'Manage repository'. 5. An error similar like this one appears: Error Traceback: View as: Interactive | Text | XML (full) â ValueError: invalid literal for int() with base 10: 'a9975dcda42e2b00' URL: http://localhost/admin_toolshed/manage_repository?id=3f428053038c8626b08a92… Module weberror.evalexception.middleware:364 in respond view >> app_iter = self.application(environ, detect_start_response) Module paste.recursive:84 in __call__ view >> return self.application(environ, start_response) Module paste.httpexceptions:633 in __call__ view >> return self.application(environ, start_response) Module galaxy.web.framework.base:132 in __call__ view >> return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:190 in handle_request view >> body = method( trans, **kwargs ) Module galaxy.web.framework:221 in decorator view >> return func( self, trans, *args, **kwargs ) Module galaxy.webapps.galaxy.controllers.admin_toolshed:561 in manage_repository view >> repository = suc.get_installed_tool_shed_repository( trans, repository_id ) Module tool_shed.util.shed_util_common:513 in get_installed_tool_shed_repository view >> return trans.sa_session.query( trans.model.ToolShedRepository ).get( trans.security.decode_id( id ) ) Module galaxy.web.security:60 in decode_id view >> return int( self.id_cipher.decrypt( obj_id.decode( 'hex' ) ).lstrip( "!" ) ) ValueError: invalid literal for int() with base 10: 'a9975dcda42e2b00' All tools with dependencies seem to have this behaviour. Cheers, Joachim -- Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team

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