Re: [galaxy-dev] Default history
Hi Jordi Have you looked into using "Data Libraries", see: http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Libraries http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files Your anonymous users can then select any of the prepared data sets (via the 'Shared Data' tab), and easily import them into their histories without data duplication. Regards, Hans On 06/19/2013 09:32 PM, Jordi Vaquero wrote: 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 ___ 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/ ___ 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/
Re: [galaxy-dev] Developing Tools
Hi Saliya, the Galaxy documentation is a good starting point for your questions: http://wiki.galaxyproject.org/ http://wiki.galaxyproject.org/Admin/Tools/Add%20Tool%20Tutorial Also have a look at the Tool Shed: http://wiki.galaxyproject.org/Admin/Tools/Add%20Tool%20Tutorial You can search for Galaxy related topics with: http://galaxyproject.org/search/web/ Hope that helps as starting point. Galaxy will take care for your cluster integration. Cheers, Bjoern > 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 esal...@gmail.com > Cell 812-391-4914 Home 812-961-6383 > http://saliya.org > ___ > 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/ ___ 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/
Re: [galaxy-dev] visulaization tool
Hi james, 49: 1.bigwig 20.7 KB format: bigwig, database: ? uploaded bigwig file display in IGB Local Web I have uploaded 1.bigwig file in this https://main.g2.bx.psu.edu/ galaxy . but when i clicked Web option . it creates a ".jnlp" file . I am not able to see anything on web . how the local option works in this case ? regards shashi From: shashi shekhar To: James Taylor Cc: "galaxy-dev@lists.bx.psu.edu" Sent: Thursday, 20 June 2013 11:50 AM Subject: Re: [galaxy-dev] visulaization tool Hi james, can you share some examples of display application . and in which tool you use for display application in galaxy ? Regards shashi From: James Taylor To: shashi shekhar Cc: Ross ; "galaxy-dev@lists.bx.psu.edu" Sent: Wednesday, 19 June 2013 7:03 PM Subject: Re: [galaxy-dev] visulaization tool Tightly integrated interactive visualizations like Trackster need to be web based (implemented in Javascript). See our paper that just came out in BMC genomics. Note there is already a phylogenetic tree visualization tool (phyloviz) that was built by Tomithy Too. Extensions to that for additional features would be welcome. For a Java based visualization tool you need to take a completely different approach. Look at Display Applications support, specifically examples like IGB and IGV. On Jun 19, 2013, at 7:56 AM, shashi shekhar wrote: Hi Ross, >Actually i have to add the visualization which will be interactive . it >will take dataset from galaxy .it will be in the same way as tracker works . >in stead of tracker i want to add my own visualization tool. from wehere >should i start to replace tracker with my own visulization tool. >Regards >shashi > > > > > From: Ross >To: shashi shekhar >Cc: Hans-Rudolf Hotz ; "galaxy-dev@lists.bx.psu.edu" > >Sent: Wednesday, 19 June 2013 5:02 PM >Subject: Re: [galaxy-dev] visulaization tool > > > >Shashi, >Thanks for the additional information. >AFAIK: If it's command line driven and spews out pdf's, adapt any similar tool >that spews out pdfs like fastqc. >Galaxy tool execution is isolated from the user and from Galaxy itself, so >communication is just not possible if it's interactive - unless you hack the >tool into Galaxy itself or something. There is no documentation for that. > > > > > >On Wed, Jun 19, 2013 at 9:01 PM, shashi shekhar >wrote: > >Hi Ross, >>thanks for the reply . actually i want to use TreeView as visulaization tool. >> >> >> >>TreeView X is an open source and multi-platform program to display >>phylogenetic trees. It can read and display NEXUS and Newick format tree >>files (such as those output by PAUP*, ClustalX, TREE-PUZZLE, and other >>programs). It allows one to order the branches of the trees, and to export >>the trees in SVG format. >> >> >>i have to add treeviewx in galaxy.. >> >> >>Regardsshashi >> >> >> >> >> >> >> From: Ross >>To: shashi shekhar >>Cc: Hans-Rudolf Hotz ; "galaxy-dev@lists.bx.psu.edu" >> >>Sent: Wednesday, 19 June 2013 3:28 PM >> >>Subject: Re: [galaxy-dev] visulaization tool >> >> >> >>Shashi, >>Hans made a brave guess based on your vague question, but you'll probably get >>better answers if you do us all a favour and make an effort to provide >>unambiguous detail about exactly what you want to achieve. >> >> >>If there is a working Galaxy tool that does what you need but using a >>different "visualisation program" (whatever you mean by that vague term), >>substituting your executable will probably be relatively trivial. eg do you >>consider the Html object produced by the fastqc or the image from the >>scatterplot tool to be "visualisation program" outputs? If so, clone a >>working tool. >> >> >> >> >>On Wed, Jun 19, 2013 at 5:37 PM, shashi shekhar >>wrote: >> >> >>> >>>Hi, >>> >>> >>>I want to add the the complete separate tool in galaxy . how will i do it >>>..i don't want to use existing visulaization tool. >>> >>> >>>Regardsshashi >>> >>> >>> >>> >>> From: Hans-Rudolf Hotz >>>To: shashi shekhar >>>Cc: "galaxy-dev@lists.bx.psu.edu" >>>Sent: Wednesday, 19 June 2013 12:29 PM >>>Subject: Re: [galaxy-dev] visulaization tool >>> >>> >>>Hi Shashi >>> >>>Have a look at: >>> >>>http://wiki.galaxyproject.org/Learn/Visualization >>>http://wiki.galaxyproject.org/Visualization%20Setup >>> >>> >>>Regards, Hans-Rudolf >>> >>> >>> >>>On 06/19/2013 08:07 AM, shashi shekhar wrote: Hi, i want to add new visualization tool in galaxy . can i get the required documents ? can u send me the details how can i add the visualization tool in galaxy . Regards shashi >>> > > > > ___ >Please keep all replies on the list by using "reply all" >in your mail client. To manage your subscriptions to this >an
Re: [galaxy-dev] visulaization tool
Hi james, can you share some examples of display application . and in which tool you use for display application in galaxy ? Regards shashi From: James Taylor To: shashi shekhar Cc: Ross ; "galaxy-dev@lists.bx.psu.edu" Sent: Wednesday, 19 June 2013 7:03 PM Subject: Re: [galaxy-dev] visulaization tool Tightly integrated interactive visualizations like Trackster need to be web based (implemented in Javascript). See our paper that just came out in BMC genomics. Note there is already a phylogenetic tree visualization tool (phyloviz) that was built by Tomithy Too. Extensions to that for additional features would be welcome. For a Java based visualization tool you need to take a completely different approach. Look at Display Applications support, specifically examples like IGB and IGV. On Jun 19, 2013, at 7:56 AM, shashi shekhar wrote: Hi Ross, >Actually i have to add the visualization which will be interactive . it >will take dataset from galaxy .it will be in the same way as tracker works . >in stead of tracker i want to add my own visualization tool. from wehere >should i start to replace tracker with my own visulization tool. >Regards >shashi > > > > > From: Ross >To: shashi shekhar >Cc: Hans-Rudolf Hotz ; "galaxy-dev@lists.bx.psu.edu" > >Sent: Wednesday, 19 June 2013 5:02 PM >Subject: Re: [galaxy-dev] visulaization tool > > > >Shashi, >Thanks for the additional information. >AFAIK: If it's command line driven and spews out pdf's, adapt any similar tool >that spews out pdfs like fastqc. >Galaxy tool execution is isolated from the user and from Galaxy itself, so >communication is just not possible if it's interactive - unless you hack the >tool into Galaxy itself or something. There is no documentation for that. > > > > > >On Wed, Jun 19, 2013 at 9:01 PM, shashi shekhar >wrote: > >Hi Ross, >>thanks for the reply . actually i want to use TreeView as visulaization tool. >> >> >> >>TreeView X is an open source and multi-platform program to display >>phylogenetic trees. It can read and display NEXUS and Newick format tree >>files (such as those output by PAUP*, ClustalX, TREE-PUZZLE, and other >>programs). It allows one to order the branches of the trees, and to export >>the trees in SVG format. >> >> >>i have to add treeviewx in galaxy.. >> >> >>Regardsshashi >> >> >> >> >> >> >> From: Ross >>To: shashi shekhar >>Cc: Hans-Rudolf Hotz ; "galaxy-dev@lists.bx.psu.edu" >> >>Sent: Wednesday, 19 June 2013 3:28 PM >> >>Subject: Re: [galaxy-dev] visulaization tool >> >> >> >>Shashi, >>Hans made a brave guess based on your vague question, but you'll probably get >>better answers if you do us all a favour and make an effort to provide >>unambiguous detail about exactly what you want to achieve. >> >> >>If there is a working Galaxy tool that does what you need but using a >>different "visualisation program" (whatever you mean by that vague term), >>substituting your executable will probably be relatively trivial. eg do you >>consider the Html object produced by the fastqc or the image from the >>scatterplot tool to be "visualisation program" outputs? If so, clone a >>working tool. >> >> >> >> >>On Wed, Jun 19, 2013 at 5:37 PM, shashi shekhar >>wrote: >> >> >>> >>>Hi, >>> >>> >>>I want to add the the complete separate tool in galaxy . how will i do it >>>..i don't want to use existing visulaization tool. >>> >>> >>>Regardsshashi >>> >>> >>> >>> >>> From: Hans-Rudolf Hotz >>>To: shashi shekhar >>>Cc: "galaxy-dev@lists.bx.psu.edu" >>>Sent: Wednesday, 19 June 2013 12:29 PM >>>Subject: Re: [galaxy-dev] visulaization tool >>> >>> >>>Hi Shashi >>> >>>Have a look at: >>> >>>http://wiki.galaxyproject.org/Learn/Visualization >>>http://wiki.galaxyproject.org/Visualization%20Setup >>> >>> >>>Regards, Hans-Rudolf >>> >>> >>> >>>On 06/19/2013 08:07 AM, shashi shekhar wrote: Hi, i want to add new visualization tool in galaxy . can i get the required documents ? can u send me the details how can i add the visualization tool in galaxy . Regards shashi >>> > > > > ___ >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/___ 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/
[galaxy-dev] Developing Tools
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 esal...@gmail.com Cell 812-391-4914 Home 812-961-6383 http://saliya.org ___ 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/
Re: [galaxy-dev] Messed up a tool installation from a local toolshed
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 | 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://localhost:9009/&repository_ids=84cbaf0b6bf7a1a9&changeset_revisions=fc2339abcab7 > 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 | 38
Re: [galaxy-dev] Possible bug in managing tool shed repositories
Hello Joachim and Björn, This issue should be resolved in change set 10103:d842d50a6ed3, which is currently running on the test tool shed. Thanks fro reporting this! Greg Von Kuster On Jun 19, 2013, at 6:16 AM, Björn Grüning wrote: > Hi Joachim, > > confirmed, it seems like a bug. > > Cheers, > Björn > > >> 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=3f428053038c8626b08a92869ee1362d132430354fe813e0 >> 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 >> > > > > ___ > 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/ > ___ 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/
[galaxy-dev] Default history
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 ___ 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/
[galaxy-dev] nglims roles
Hi, what roles are embedded in nglims? (am I calling it by the right name?) I have a "sequencing" role which will be given to anyone submitting a request, and that seems to be working just fine. I am also using the yaml form to edit the submission form, and I think it's beautifully implemented. However, I cannot figure out how someone on our MiSeq team will access the submissions unless they are admins of Galaxy. I would like to avoid this situation because the MiSeq team should not have the same permissions that allows them to view all data or install new tools. Is there a role that I can give someone who is actually performing the sequencing? And what would it be? -- Lee Katz, Ph.D. ___ 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/
[galaxy-dev] Panels disappearing when choosing tools
Hi all,
Again a question from my side in connection with setting up a new Galaxy
instance within an closed network (including a proxy) an SLES 11 SP2.
After some struggeling with the Apache config finally Galaxy was
accessible, but behaves somewhat strange compared to another instance
which is running for a long time without complains (and which was
recently updated to the june release).
When I choose a tool from the panel on the left side everything works
fine until I click on the corresponding link. Unlike the usual case the
tools 'GUI' (so the wrapper web page) appears within Galaxy's central
pane this side get's 'full screened', means: the panels left (tools),
right (history) and on the top side (navigation) are not shown any more.
It does not matter wether I'm logged in or not (Galaxy can be accessed
by guests currently).
Due to the Apache stuff before I compared the access logs of this new
instance an the established one: they definitly look different...
'correct':
[IP1] - galaxy [19/Jun/2013:19:11:22 +0200] "GET
/galaxy/static/style/library.css?v=1370962215 HTTP/1.1" 200 1237
"https://[url]/galaxy/tool_runner?tool_id=upload1"; "Mozilla/5.0 (X11;
Linux i686)
AppleWebKit/537.4 (KHTML, like Gecko) Ubuntu/12.10 Chromium/22.0.1229.94
Chrome/22.0.1229.94 Safari/537.4"
'somewhat strange':
[IP2] - - [19/Jun/2013:19:23:16 +0200] "GET
/galaxy/tool_runner?tool_id=upload1 HTTP/1.1" 200 35869
Access was performed from the same maschine, using the same browser.
What I see is that on the one hand the second field which follows the IP
(removed here) is filled with 'galaxy' in the first case, but empty
('-') in the second one. On the other hand it is obvious that most of
the info around e.g the accessing browser etc. is missing. The error log
does not note anything during this access.
Due to the fact that I'm nearly right the opposite of a webserver god
(but willed to learn) I would really appreciate your help to fix this.
Thanks in advance,
Sebastian
--
Sebastian Schaaf, M.Sc. Bioinformatics
University of Munich
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Re: [galaxy-dev] visulaization tool
Tightly integrated interactive visualizations like Trackster need to be web based (implemented in Javascript). See our paper that just came out in BMC genomics. Note there is already a phylogenetic tree visualization tool (phyloviz) that was built by Tomithy Too. Extensions to that for additional features would be welcome. For a Java based visualization tool you need to take a completely different approach. Look at Display Applications support, specifically examples like IGB and IGV. On Jun 19, 2013, at 7:56 AM, shashi shekhar wrote: > Hi Ross, > Actually i have to add the visualization which will be interactive . it > will take dataset from galaxy .it will be in the same way as tracker works . > in stead of tracker i want to add my own visualization tool. from wehere > should i start to replace tracker with my own visulization tool. > Regards > shashi > > From: Ross > To: shashi shekhar > Cc: Hans-Rudolf Hotz ; "galaxy-dev@lists.bx.psu.edu" > > Sent: Wednesday, 19 June 2013 5:02 PM > Subject: Re: [galaxy-dev] visulaization tool > > Shashi, > Thanks for the additional information. > AFAIK: If it's command line driven and spews out pdf's, adapt any similar > tool that spews out pdfs like fastqc. > Galaxy tool execution is isolated from the user and from Galaxy itself, so > communication is just not possible if it's interactive - unless you hack the > tool into Galaxy itself or something. There is no documentation for that. > > > > On Wed, Jun 19, 2013 at 9:01 PM, shashi shekhar > wrote: > Hi Ross, > thanks for the reply . actually i want to use TreeView as visulaization tool. > > TreeView X is an open source and multi-platform program to display > phylogenetic trees. It can read and display NEXUS and Newick format tree > files (such as those output by PAUP*, ClustalX, TREE-PUZZLE, and other > programs). It allows one to order the branches of the trees, and to export > the trees in SVG format. > > i have to add treeviewx in galaxy.. > > Regards > shashi > > > From: Ross > To: shashi shekhar > Cc: Hans-Rudolf Hotz ; "galaxy-dev@lists.bx.psu.edu" > > Sent: Wednesday, 19 June 2013 3:28 PM > > Subject: Re: [galaxy-dev] visulaization tool > > Shashi, > Hans made a brave guess based on your vague question, but you'll probably get > better answers if you do us all a favour and make an effort to provide > unambiguous detail about exactly what you want to achieve. > > If there is a working Galaxy tool that does what you need but using a > different "visualisation program" (whatever you mean by that vague term), > substituting your executable will probably be relatively trivial. eg do you > consider the Html object produced by the fastqc or the image from the > scatterplot tool to be "visualisation program" outputs? If so, clone a > working tool. > > > On Wed, Jun 19, 2013 at 5:37 PM, shashi shekhar > wrote: > > Hi, > > I want to add the the complete separate tool in galaxy . how will i do it ..i > don't want to use existing visulaization tool. > > Regards > shashi > > From: Hans-Rudolf Hotz > To: shashi shekhar > Cc: "galaxy-dev@lists.bx.psu.edu" > Sent: Wednesday, 19 June 2013 12:29 PM > Subject: Re: [galaxy-dev] visulaization tool > > Hi Shashi > > Have a look at: > > http://wiki.galaxyproject.org/Learn/Visualization > http://wiki.galaxyproject.org/Visualization%20Setup > > > Regards, Hans-Rudolf > > > > On 06/19/2013 08:07 AM, shashi shekhar wrote: > > Hi, > > > > i want to add new visualization tool in galaxy . can i get the required > > documents ? > > > > can u send me the details how can i add the visualization tool in galaxy . > > > > > > > > Regards > > shashi > > > > > ___ > 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/ ___ 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/
[galaxy-dev] displaying further input based on previous input
Hi all, I am trying to format the input to a java tool that I am writing. I want to display different options to choose from based on the user input. I am not sure how to do that. For example, based on the input file, I want to display the chromosome options to choose from. How do I do this? chr1 chr2 I am not sure how to call a program that will generate the second input based on the first one and then wait for the user to choose the rest of the input and then run another program. I am a newbie. Any help is appreciated! Thanks, VJ. ___ 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/
Re: [galaxy-dev] visulaization tool
Hi Ross i got the file registry.py in lib/galaxy/visualization directory .. here four built in visualization is mentioned ..in the same way i want to add one more VISUALIZATION in galaxy ...this is my question . i wanted tom know that from which files i should start . class VisualizationsRegistry( object ): """ Main responsibilities are: - testing if an object has a visualization that can be applied to it - generating a link to controllers.visualization.render with the appropriate params - validating and parsing params into resources (based on a context) used in the visualization template """ # these should be handled somewhat differently - and be passed onto their resp. methods in ctrl.visualization #TODO: change/remove if/when they can be updated to use this system BUILT_IN_VISUALIZATIONS = [ ] # where to search for visualiztion templates (relative to templates/webapps/galaxy) # this can be overridden individually in the config entries Regards shashi From: Ross To: shashi shekhar Cc: "galaxy-dev@lists.bx.psu.edu" Sent: Wednesday, 19 June 2013 5:32 PM Subject: Re: [galaxy-dev] visulaization tool Shashi, Beats me. Cloning the visualisation code would be a good start I'd guess. It will not be trivial. Others may have better ideas. On Wed, Jun 19, 2013 at 9:56 PM, shashi shekhar wrote: Hi Ross, >Actually i have to add the visualization which will be interactive . it >will take dataset from galaxy .it will be in the same way as tracker works . >in stead of tracker i want to add my own visualization tool. from wehere >should i start to replace tracker with my own visulization tool. >Regards >shashi > > > > > From: Ross >To: shashi shekhar >Cc: Hans-Rudolf Hotz ; "galaxy-dev@lists.bx.psu.edu" > >Sent: Wednesday, 19 June 2013 5:02 PM > >Subject: Re: [galaxy-dev] visulaization tool > > > >Shashi, >Thanks for the additional information. >AFAIK: If it's command line driven and spews out pdf's, adapt any similar tool >that spews out pdfs like fastqc. >Galaxy tool execution is isolated from the user and from Galaxy itself, so >communication is just not possible if it's interactive - unless you hack the >tool into Galaxy itself or something. There is no documentation for that. > > > > > >On Wed, Jun 19, 2013 at 9:01 PM, shashi shekhar >wrote: > >Hi Ross, >>thanks for the reply . actually i want to use TreeView as visulaization tool. >> >> >> >>TreeView X is an open source and multi-platform program to display >>phylogenetic trees. It can read and display NEXUS and Newick format tree >>files (such as those output by PAUP*, ClustalX, TREE-PUZZLE, and other >>programs). It allows one to order the branches of the trees, and to export >>the trees in SVG format. >> >> >>i have to add treeviewx in galaxy.. >> >> >>Regardsshashi >> >> >> >> >> >> >> From: Ross >>To: shashi shekhar >>Cc: Hans-Rudolf Hotz ; "galaxy-dev@lists.bx.psu.edu" >> >>Sent: Wednesday, 19 June 2013 3:28 PM >> >>Subject: Re: [galaxy-dev] visulaization tool >> >> >> >>Shashi, >>Hans made a brave guess based on your vague question, but you'll probably get >>better answers if you do us all a favour and make an effort to provide >>unambiguous detail about exactly what you want to achieve. >> >> >>If there is a working Galaxy tool that does what you need but using a >>different "visualisation program" (whatever you mean by that vague term), >>substituting your executable will probably be relatively trivial. eg do you >>consider the Html object produced by the fastqc or the image from the >>scatterplot tool to be "visualisation program" outputs? If so, clone a >>working tool. >> >> >> >> >>On Wed, Jun 19, 2013 at 5:37 PM, shashi shekhar >>wrote: >> >> >>> >>>Hi, >>> >>> >>>I want to add the the complete separate tool in galaxy . how will i do it >>>..i don't want to use existing visulaization tool. >>> >>> >>>Regardsshashi >>> >>> >>> >>> >>> From: Hans-Rudolf Hotz >>>To: shashi shekhar >>>Cc: "galaxy-dev@lists.bx.psu.edu" >>>Sent: Wednesday, 19 June 2013 12:29 PM >>>Subject: Re: [galaxy-dev] visulaization tool >>> >>> >>>Hi Shashi >>> >>>Have a look at: >>> >>>http://wiki.galaxyproject.org/Learn/Visualization >>>http://wiki.galaxyproject.org/Visualization%20Setup >>> >>> >>>Regards, Hans-Rudolf >>> >>> >>> >>>On 06/19/2013 08:07 AM, shashi shekhar wrote: Hi, i want to add new visualization tool in galaxy . can i get the required documents ? can u send me the details how can i add the visualization tool in galaxy . Regards shashi >>> > > > >___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this an
Re: [galaxy-dev] visulaization tool
Shashi, Beats me. Cloning the visualisation code would be a good start I'd guess. It will not be trivial. Others may have better ideas. On Wed, Jun 19, 2013 at 9:56 PM, shashi shekhar wrote: > Hi Ross, > Actually i have to add the visualization which will be interactive . it > will take dataset from galaxy .it will be in the same way as tracker > works . > in stead of tracker i want to add my own visualization tool. from wehere > should i start to replace tracker with my own visulization tool. > Regards > shashi > > -- > *From:* Ross > *To:* shashi shekhar > *Cc:* Hans-Rudolf Hotz ; "galaxy-dev@lists.bx.psu.edu" < > galaxy-dev@lists.bx.psu.edu> > *Sent:* Wednesday, 19 June 2013 5:02 PM > > *Subject:* Re: [galaxy-dev] visulaization tool > > Shashi, > Thanks for the additional information. > AFAIK: If it's command line driven and spews out pdf's, adapt any similar > tool that spews out pdfs like fastqc. > Galaxy tool execution is isolated from the user and from Galaxy itself, so > communication is just not possible if it's interactive - unless you hack > the tool into Galaxy itself or something. There is no documentation for > that. > > > > On Wed, Jun 19, 2013 at 9:01 PM, shashi shekhar > wrote: > > Hi Ross, > thanks for the reply . actually i want to use TreeView as visulaization > tool. > > TreeView X is an open source and multi-platform program to display > phylogenetic trees. It can read and display NEXUS and Newick format tree > files (such as those output by PAUP*, ClustalX, TREE-PUZZLE, and other > programs). It allows one to order the branches of the trees, and to export > the trees in SVG format. > > i have to add treeviewx in galaxy.. > > Regards > shashi > > > -- > *From:* Ross > *To:* shashi shekhar > *Cc:* Hans-Rudolf Hotz ; "galaxy-dev@lists.bx.psu.edu" < > galaxy-dev@lists.bx.psu.edu> > *Sent:* Wednesday, 19 June 2013 3:28 PM > > *Subject:* Re: [galaxy-dev] visulaization tool > > Shashi, > Hans made a brave guess based on your vague question, but you'll probably > get better answers if you do us all a favour and make an effort to provide > unambiguous detail about exactly what you want to achieve. > > If there is a working Galaxy tool that does what you need but using a > different "visualisation program" (whatever you mean by that vague term), > substituting your executable will probably be relatively trivial. eg do you > consider the Html object produced by the fastqc or the image from the > scatterplot tool to be "visualisation program" outputs? If so, clone a > working tool. > > > On Wed, Jun 19, 2013 at 5:37 PM, shashi shekhar > wrote: > > > Hi, > > I want to add the the complete separate tool in galaxy . how will i do it > ..i don't want to use existing visulaization tool. > > Regards > shashi > > -- > *From:* Hans-Rudolf Hotz > *To:* shashi shekhar > *Cc:* "galaxy-dev@lists.bx.psu.edu" > *Sent:* Wednesday, 19 June 2013 12:29 PM > *Subject:* Re: [galaxy-dev] visulaization tool > > Hi Shashi > > Have a look at: > > http://wiki.galaxyproject.org/Learn/Visualization > http://wiki.galaxyproject.org/Visualization%20Setup > > > Regards, Hans-Rudolf > > > > On 06/19/2013 08:07 AM, shashi shekhar wrote: > > Hi, > > > > i want to add new visualization tool in galaxy . can i get the required > > documents ? > > > > can u send me the details how can i add the visualization tool in > galaxy . > > > > > > > > Regards > > shashi > > > > > > ___ 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/
Re: [galaxy-dev] visulaization tool
Hi Ross, Actually i have to add the visualization which will be interactive . it will take dataset from galaxy .it will be in the same way as tracker works . in stead of tracker i want to add my own visualization tool. from wehere should i start to replace tracker with my own visulization tool. Regards shashi From: Ross To: shashi shekhar Cc: Hans-Rudolf Hotz ; "galaxy-dev@lists.bx.psu.edu" Sent: Wednesday, 19 June 2013 5:02 PM Subject: Re: [galaxy-dev] visulaization tool Shashi, Thanks for the additional information. AFAIK: If it's command line driven and spews out pdf's, adapt any similar tool that spews out pdfs like fastqc. Galaxy tool execution is isolated from the user and from Galaxy itself, so communication is just not possible if it's interactive - unless you hack the tool into Galaxy itself or something. There is no documentation for that. On Wed, Jun 19, 2013 at 9:01 PM, shashi shekhar wrote: Hi Ross, >thanks for the reply . actually i want to use TreeView as visulaization tool. > > > >TreeView X is an open source and multi-platform program to display >phylogenetic trees. It can read and display NEXUS and Newick format tree files >(such as those output by PAUP*, ClustalX, TREE-PUZZLE, and other programs). It >allows one to order the branches of the trees, and to export the trees in SVG >format. > > >i have to add treeviewx in galaxy.. > > >Regardsshashi > > > > > > > From: Ross >To: shashi shekhar >Cc: Hans-Rudolf Hotz ; "galaxy-dev@lists.bx.psu.edu" > >Sent: Wednesday, 19 June 2013 3:28 PM > >Subject: Re: [galaxy-dev] visulaization tool > > > >Shashi, >Hans made a brave guess based on your vague question, but you'll probably get >better answers if you do us all a favour and make an effort to provide >unambiguous detail about exactly what you want to achieve. > > >If there is a working Galaxy tool that does what you need but using a >different "visualisation program" (whatever you mean by that vague term), >substituting your executable will probably be relatively trivial. eg do you >consider the Html object produced by the fastqc or the image from the >scatterplot tool to be "visualisation program" outputs? If so, clone a working >tool. > > > > >On Wed, Jun 19, 2013 at 5:37 PM, shashi shekhar >wrote: > > >> >>Hi, >> >> >>I want to add the the complete separate tool in galaxy . how will i do it ..i >>don't want to use existing visulaization tool. >> >> >>Regardsshashi >> >> >> >> >> From: Hans-Rudolf Hotz >>To: shashi shekhar >>Cc: "galaxy-dev@lists.bx.psu.edu" >>Sent: Wednesday, 19 June 2013 12:29 PM >>Subject: Re: [galaxy-dev] visulaization tool >> >> >>Hi Shashi >> >>Have a look at: >> >>http://wiki.galaxyproject.org/Learn/Visualization >>http://wiki.galaxyproject.org/Visualization%20Setup >> >> >>Regards, Hans-Rudolf >> >> >> >>On 06/19/2013 08:07 AM, shashi shekhar wrote: >>> Hi, >>> >>> i want to add new visualization tool in galaxy . can i get the required >>> documents ? >>> >>> can u send me the details how can i add the visualization tool in galaxy . >>> >>> >>> >>> Regards >>> shashi >>___ 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/
Re: [galaxy-dev] visulaization tool
Shashi, Thanks for the additional information. AFAIK: If it's command line driven and spews out pdf's, adapt any similar tool that spews out pdfs like fastqc. Galaxy tool execution is isolated from the user and from Galaxy itself, so communication is just not possible if it's interactive - unless you hack the tool into Galaxy itself or something. There is no documentation for that. On Wed, Jun 19, 2013 at 9:01 PM, shashi shekhar wrote: > Hi Ross, > thanks for the reply . actually i want to use TreeView as visulaization > tool. > > TreeView X is an open source and multi-platform program to display > phylogenetic trees. It can read and display NEXUS and Newick format tree > files (such as those output by PAUP*, ClustalX, TREE-PUZZLE, and other > programs). It allows one to order the branches of the trees, and to export > the trees in SVG format. > > i have to add treeviewx in galaxy.. > > Regards > shashi > > > -- > *From:* Ross > *To:* shashi shekhar > *Cc:* Hans-Rudolf Hotz ; "galaxy-dev@lists.bx.psu.edu" < > galaxy-dev@lists.bx.psu.edu> > *Sent:* Wednesday, 19 June 2013 3:28 PM > > *Subject:* Re: [galaxy-dev] visulaization tool > > Shashi, > Hans made a brave guess based on your vague question, but you'll probably > get better answers if you do us all a favour and make an effort to provide > unambiguous detail about exactly what you want to achieve. > > If there is a working Galaxy tool that does what you need but using a > different "visualisation program" (whatever you mean by that vague term), > substituting your executable will probably be relatively trivial. eg do you > consider the Html object produced by the fastqc or the image from the > scatterplot tool to be "visualisation program" outputs? If so, clone a > working tool. > > > On Wed, Jun 19, 2013 at 5:37 PM, shashi shekhar > wrote: > > > Hi, > > I want to add the the complete separate tool in galaxy . how will i do it > ..i don't want to use existing visulaization tool. > > Regards > shashi > > -- > *From:* Hans-Rudolf Hotz > *To:* shashi shekhar > *Cc:* "galaxy-dev@lists.bx.psu.edu" > *Sent:* Wednesday, 19 June 2013 12:29 PM > *Subject:* Re: [galaxy-dev] visulaization tool > > Hi Shashi > > Have a look at: > > http://wiki.galaxyproject.org/Learn/Visualization > http://wiki.galaxyproject.org/Visualization%20Setup > > > Regards, Hans-Rudolf > > > > On 06/19/2013 08:07 AM, shashi shekhar wrote: > > Hi, > > > > i want to add new visualization tool in galaxy . can i get the required > > documents ? > > > > can u send me the details how can i add the visualization tool in > galaxy . > > > > > > > > Regards > > shashi > > ___ 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/
Re: [galaxy-dev] visulaization tool
Hi Ross, thanks for the reply . actually i want to use TreeView as visulaization tool. TreeView X is an open source and multi-platform program to display phylogenetic trees. It can read and display NEXUS and Newick format tree files (such as those output by PAUP*, ClustalX, TREE-PUZZLE, and other programs). It allows one to order the branches of the trees, and to export the trees in SVG format. i have to add treeviewx in galaxy.. Regards shashi From: Ross To: shashi shekhar Cc: Hans-Rudolf Hotz ; "galaxy-dev@lists.bx.psu.edu" Sent: Wednesday, 19 June 2013 3:28 PM Subject: Re: [galaxy-dev] visulaization tool Shashi, Hans made a brave guess based on your vague question, but you'll probably get better answers if you do us all a favour and make an effort to provide unambiguous detail about exactly what you want to achieve. If there is a working Galaxy tool that does what you need but using a different "visualisation program" (whatever you mean by that vague term), substituting your executable will probably be relatively trivial. eg do you consider the Html object produced by the fastqc or the image from the scatterplot tool to be "visualisation program" outputs? If so, clone a working tool. On Wed, Jun 19, 2013 at 5:37 PM, shashi shekhar wrote: > >Hi, > > >I want to add the the complete separate tool in galaxy . how will i do it ..i >don't want to use existing visulaization tool. > > >Regardsshashi > > > > > From: Hans-Rudolf Hotz >To: shashi shekhar >Cc: "galaxy-dev@lists.bx.psu.edu" >Sent: Wednesday, 19 June 2013 12:29 PM >Subject: Re: [galaxy-dev] visulaization tool > > >Hi Shashi > >Have a look at: > >http://wiki.galaxyproject.org/Learn/Visualization >http://wiki.galaxyproject.org/Visualization%20Setup > > >Regards, Hans-Rudolf > > > >On 06/19/2013 08:07 AM, shashi shekhar wrote: >> Hi, >> >> i want to add new visualization tool in galaxy . can i get the required >> documents ? >> >> can u send me the details how can i add the visualization tool in galaxy . >> >> >> >> Regards >> shashi >> >> >> ___ >> 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/ >> > >___ 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/
Re: [galaxy-dev] Possible bug in managing tool shed repositories
Hi Joachim, confirmed, it seems like a bug. Cheers, Björn > 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=3f428053038c8626b08a92869ee1362d132430354fe813e0 > 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 > ___ 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/
Re: [galaxy-dev] Startup error, Galaxy DB got corrupted?
Dear Dannon, Thanks for your suggestion! We did give it a try with the backup copy of 10 days back and that worked! We keep the postgres log and the failed postgres backup (using pg_dump with both custom and plain text format) for now and will look into what exactly happened during those 10 days. After this update, it seems we also have solved the problem of missing user email addresses in the add quota page. Need a bit more test further to see it all goes well. Cheers, Leon On Tue, Jun 18, 2013 at 3:24 AM, Dannon Baker wrote: > The error "ERROR: could not read block 326 in file "base/257536/259291": > read only 0 of 8192 bytes" line makes me wonder if your database may have > been corrupt prior to the upgrade/dump. Some brief googling suggests that > this could be hardware failure induced among other things. Can you check > the postgres logs for any likely explanations? > > How exactly did you perform your database backup and attempted recreation? > > -Dannon > > > On Mon, Jun 17, 2013 at 5:12 PM, Leon Mei wrote: > >> Dear list, >> >> Yesterday, I noticed that the user quota setting on our Galaxy had a >> problem - the list of user email address is missing from the manage quota >> page. So I thought to give a Galaxy codebase update a try after backing up >> the Galaxy dir and the database. >> >> Running hg head gives me: >> == >> postgres@ubuntu:/mnt/galaxyTools/galaxy-2013-05-13$ hg head >> changeset: 10003:b4a373d86c51 >> tag: tip >> parent: 10001:471484ff8be6 >> user:greg >> date:Wed Jun 12 11:48:09 2013 -0400 >> summary: Add targets to Repository Actions menu items. >> == >> >> I updated the DB schema to support the code update. But the restart of >> Galaxy failed with an error in paster.log: >> == >> Traceback (most recent call last): >> File >> "/mnt/galaxyTools/galaxy-2013-05-13/lib/galaxy/webapps/galaxy/buildapp.py", >> line 35, in app_factory >> app = UniverseApplication( global_conf = global_conf, **kwargs ) >> File "/mnt/galaxyTools/galaxy-2013-05-13/lib/galaxy/app.py", line 164, >> in __init__ >> self.job_manager = manager.JobManager( self ) >> File "/mnt/galaxyTools/galaxy-2013-05-13/lib/galaxy/jobs/manager.py", >> line 36, in __init__ >> self.job_handler.start() >> File "/mnt/galaxyTools/galaxy-2013-05-13/lib/galaxy/jobs/handler.py", >> line 34, in start >> self.job_queue.start() >> File "/mnt/galaxyTools/galaxy-2013-05-13/lib/galaxy/jobs/handler.py", >> line 77, in start >> self.__check_jobs_at_startup() >> File "/mnt/galaxyTools/galaxy-2013-05-13/lib/galaxy/jobs/handler.py", >> line 125, in __check_jobs_at_startup >> self.dispatcher.recover( job, job_wrapper ) >> File "/mnt/galaxyTools/galaxy-2013-05-13/lib/galaxy/jobs/handler.py", >> line 620, in recover >> self.job_runners[runner_name].recover( job, job_wrapper ) >> File >> "/mnt/galaxyTools/galaxy-2013-05-13/lib/galaxy/jobs/runners/local.py", line >> 128, in recover >> job_wrapper.change_state( model.Job.states.ERROR, info = "This job >> was killed when Galaxy was restarted. Please retry the job." ) >> File "/mnt/galaxyTools/galaxy-2013-05-13/lib/galaxy/jobs/__init__.py", >> line 824, in change_state >> dataset.state = state >> File "/mnt/galaxyTools/galaxy-2013-05-13/lib/galaxy/model/__init__.py", >> line 1163, in set_dataset_state >> object_session( self ).flush() #flush here, because hda.flush() won't >> flush the Dataset object >> File >> "/mnt/galaxyTools/galaxy-2013-05-13/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", >> line 1718, in flush >> self._flush(objects) >> File >> "/mnt/galaxyTools/galaxy-2013-05-13/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", >> line 1789, in _flush >> flush_context.execute() >> File >> "/mnt/galaxyTools/galaxy-2013-05-13/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/unitofwork.py", >> line 331, in execute >> rec.execute(self) >> File >> "/mnt/galaxyTools/galaxy-2013-05-13/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/unitofwork.py", >> line 475, in execute >> uow >> File >> "/mnt/galaxyTools/galaxy-2013-05-13/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/persistence.py", >> line 59, in save_obj >> mapper, table, update) >> File >> "/mnt/galaxyTools/galaxy-2013-05-13/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/persistence.py", >> line 485, in _emit_update_statements >> execute(statement, params) >> File >> "/mnt/galaxyTools/galaxy-2013-05-13/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", >> line 1449, in execute >> params) >> File >> "/mnt/galaxyTools/galaxy-2013-05-13/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", >> line 1584, in _execute_clauseelement >> compiled_sql, distilled_params >> File >> "/mnt/galaxyTools/galaxy-2013-05-13/eggs/SQLAlche
Re: [galaxy-dev] visulaization tool
Shashi, Hans made a brave guess based on your vague question, but you'll probably get better answers if you do us all a favour and make an effort to provide unambiguous detail about exactly what you want to achieve. If there is a working Galaxy tool that does what you need but using a different "visualisation program" (whatever you mean by that vague term), substituting your executable will probably be relatively trivial. eg do you consider the Html object produced by the fastqc or the image from the scatterplot tool to be "visualisation program" outputs? If so, clone a working tool. On Wed, Jun 19, 2013 at 5:37 PM, shashi shekhar wrote: > > Hi, > > I want to add the the complete separate tool in galaxy . how will i do it > ..i don't want to use existing visulaization tool. > > Regards > shashi > > -- > *From:* Hans-Rudolf Hotz > *To:* shashi shekhar > *Cc:* "galaxy-dev@lists.bx.psu.edu" > *Sent:* Wednesday, 19 June 2013 12:29 PM > *Subject:* Re: [galaxy-dev] visulaization tool > > Hi Shashi > > Have a look at: > > http://wiki.galaxyproject.org/Learn/Visualization > http://wiki.galaxyproject.org/Visualization%20Setup > > > Regards, Hans-Rudolf > > > > On 06/19/2013 08:07 AM, shashi shekhar wrote: > > Hi, > > > > i want to add new visualization tool in galaxy . can i get the required > > documents ? > > > > can u send me the details how can i add the visualization tool in > galaxy . > > > > > > > > Regards > > shashi > > > > > > ___ > > 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/ > > > > ___ 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/
[galaxy-dev] Possible bug in managing tool shed repositories
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=3f428053038c8626b08a92869ee1362d132430354fe813e0 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 ___ 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/
Re: [galaxy-dev] visulaization tool
Hi, I want to add the the complete separate tool in galaxy . how will i do it ..i don't want to use existing visulaization tool. Regards shashi From: Hans-Rudolf Hotz To: shashi shekhar Cc: "galaxy-dev@lists.bx.psu.edu" Sent: Wednesday, 19 June 2013 12:29 PM Subject: Re: [galaxy-dev] visulaization tool Hi Shashi Have a look at: http://wiki.galaxyproject.org/Learn/Visualization http://wiki.galaxyproject.org/Visualization%20Setup Regards, Hans-Rudolf On 06/19/2013 08:07 AM, shashi shekhar wrote: > Hi, > > i want to add new visualization tool in galaxy . can i get the required > documents ? > > can u send me the details how can i add the visualization tool in galaxy . > > > > Regards > shashi > > > ___ > 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/ >___ 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/
Re: [galaxy-dev] visulaization tool
Hi Shashi Have a look at: http://wiki.galaxyproject.org/Learn/Visualization http://wiki.galaxyproject.org/Visualization%20Setup Regards, Hans-Rudolf On 06/19/2013 08:07 AM, shashi shekhar wrote: Hi, i want to add new visualization tool in galaxy . can i get the required documents ? can u send me the details how can i add the visualization tool in galaxy . Regards shashi ___ 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/ ___ 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/
