[galaxy-dev] Extra authentication
Hi, i have installed local instance of galaxy in my linux system. i want to add an extra authentication mechanism before saving user information into database in which file i have to do modification .? 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] How to enable auto option for newly added file formats
Hi, yeah i followd this tutorial .. http://wiki.galaxyproject.org/Admin/Datatypes/Adding%20Datatypes yeah ,i have tested my sniff methods .it works fine .when i upload any pdb file by using the option file format (PDB ) , it works but with auto option it doesnot work regards shashi From: Peter Cock p.j.a.c...@googlemail.com To: shashi shekhar me_shash...@yahoo.co.in Cc: Galaxy Dev galaxy-...@bx.psu.edu Sent: Tuesday, 25 June 2013 1:14 PM Subject: Re: [galaxy-dev] How to enable auto option for newly added file formats On Tue, Jun 25, 2013 at 8:28 AM, shashi shekhar me_shash...@yahoo.co.in wrote: Hi, yeah ..it is same thing... but i followed the galaxy -datatype(how to add new file format)tutorial ..but still my newly added file format is not working with auto option it always display txt format ..it is similar to txt format with some specific property .. Reagrds shashi So you've followed this: http://wiki.galaxyproject.org/Admin/Datatypes/Adding%20Datatypes Have you tested your sniff method works? Have you checked the order the file types are tested? Peter P.S. Don't forget to CC the mailing list.___ 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] How to enable auto option for newly added file formats
Hi Björn, Thanks Björn for the reply , But pdb file format is working not working auto option ..it works with by selecting PDB file format option in galaxy ... do i have to modify any registry.py file or any other file ? i have included only init ,init_meta and sniff function in PDB ( txt ) in data.py file .. Regards shahsi From: Björn Grüning bjoern.gruen...@pharmazie.uni-freiburg.de To: shashi shekhar me_shash...@yahoo.co.in Cc: Peter Cock p.j.a.c...@googlemail.com; Galaxy Dev galaxy-...@bx.psu.edu Sent: Tuesday, 25 June 2013 3:40 PM Subject: Re: [galaxy-dev] How to enable auto option for newly added file formats Hi Shashi, can you try my molecule datatype repository? http://testtoolshed.g2.bx.psu.edu/view/bgruening/chemical_datatypes The source is here: https://github.com/bgruening/galaxytools/blob/master/chemicaltoolbox/datatypes/molecules.py I have also a PDB definition inluded maybe that works for you and we can join the effort. Thanks, Bjoern Hi, yeah i followd this tutorial .. http://wiki.galaxyproject.org/Admin/Datatypes/Adding%20Datatypes yeah ,i have tested my sniff methods .it works fine .when i upload any pdb file by using the option file format (PDB ) , it works but with auto option it doesnot work regards shashi __ From: Peter Cock p.j.a.c...@googlemail.com To: shashi shekhar me_shash...@yahoo.co.in Cc: Galaxy Dev galaxy-...@bx.psu.edu Sent: Tuesday, 25 June 2013 1:14 PM Subject: Re: [galaxy-dev] How to enable auto option for newly added file formats On Tue, Jun 25, 2013 at 8:28 AM, shashi shekhar me_shash...@yahoo.co.in wrote: Hi, yeah ..it is same thing... but i followed the galaxy -datatype(how to add new file format)tutorial ..but still my newly added file format is not working with auto option it always display txt format ..it is similar to txt format with some specific property .. Reagrds shashi So you've followed this: http://wiki.galaxyproject.org/Admin/Datatypes/Adding%20Datatypes Have you tested your sniff method works? Have you checked the order the file types are tested? Peter P.S. Don't forget to CC the mailing list. ___ 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] How to enable auto option for newly added file formats
Hi, I want to enable option auto option for some format ..how will i proceed . I have alreadu added the format in galaxy ., which works without auto option. 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 James, galaxy.pdb is a dataset in galaxy , which is shown by this url http://10.180.8.54:9098/display_application/1fad1eaf5f4f1766/jmol_pdb/jmol_main/5da8464cb811e1a6/data/galaxy.pdb. i want to download this link in galaxy by using python or java . after downloading,downloaded file contains only html tags ..not the actual content . it wont's display the actual contents. Regards shashi From: James Taylor ja...@taylorlab.org To: shashi shekhar me_shash...@yahoo.co.in Cc: galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu Sent: Thursday, 20 June 2013 8:57 PM Subject: Re: [galaxy-dev] visulaization tool Display applications are extensively documented here: http://wiki.galaxyproject.org/Admin/Tools/External%20Display%20Applications%20Tutorial -- James Taylor, Assistant Professor, Biology/CS, Emory University On Thu, Jun 20, 2013 at 2:20 AM, shashi shekhar me_shash...@yahoo.co.in wrote: 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 ja...@taylorlab.org To: shashi shekhar me_shash...@yahoo.co.in Cc: Ross ross.laza...@gmail.com; galaxy-dev@lists.bx.psu.edu 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 me_shash...@yahoo.co.in 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 ross.laza...@gmail.com To: shashi shekhar me_shash...@yahoo.co.in Cc: Hans-Rudolf Hotz h...@fmi.ch; 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 me_shash...@yahoo.co.in 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 ross.laza...@gmail.com To: shashi shekhar me_shash...@yahoo.co.in Cc: Hans-Rudolf Hotz h...@fmi.ch; 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 me_shash...@yahoo.co.in 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 h...@fmi.ch To: shashi shekhar me_shash...@yahoo.co.in Cc: galaxy-dev@lists.bx.psu.edu 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
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 me_shash...@yahoo.co.in To: James Taylor ja...@taylorlab.org Cc: galaxy-dev@lists.bx.psu.edu 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 ja...@taylorlab.org To: shashi shekhar me_shash...@yahoo.co.in Cc: Ross ross.laza...@gmail.com; galaxy-dev@lists.bx.psu.edu 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 me_shash...@yahoo.co.in 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 ross.laza...@gmail.com To: shashi shekhar me_shash...@yahoo.co.in Cc: Hans-Rudolf Hotz h...@fmi.ch; 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 me_shash...@yahoo.co.in 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 ross.laza...@gmail.com To: shashi shekhar me_shash...@yahoo.co.in Cc: Hans-Rudolf Hotz h...@fmi.ch; 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 me_shash...@yahoo.co.in 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 h...@fmi.ch To: shashi shekhar me_shash...@yahoo.co.in Cc: galaxy-dev@lists.bx.psu.edu 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
Re: [galaxy-dev] visulaization tool
Hi Ross,
i am using display application as visualization in galaxy.
display id=ucsc_interval_as_bed version=1.0.0 name=display at UCSC
link id=main name=main
urlhttp://genome.ucsc.edu/cgi-bin/hgTracks?db=${qp($bed_file.dbkey)}amp;position=${position.qp}amp;hgt.customText=${bed_file.qp}/url
param type=data name=bed_file url=galaxy.bed format=bedstrict/ !--
Galaxy allows BED files to contain non-standard fields beyond the first 3
columns, UCSC does not: force use of converter which will make strict BED6+
file -- param type=template name=position strip=True
what is the meaninng param type=template name=position strip=True /
and what is the use of url=galaxy.bed ?
Regards
shashi
From: Ross ross.laza...@gmail.com
To: shashi shekhar me_shash...@yahoo.co.in
Cc: galaxy-dev@lists.bx.psu.edu 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 me_shash...@yahoo.co.in 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 ross.laza...@gmail.com
To: shashi shekhar me_shash...@yahoo.co.in
Cc: Hans-Rudolf Hotz h...@fmi.ch; 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 me_shash...@yahoo.co.in
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 ross.laza...@gmail.com
To: shashi shekhar me_shash...@yahoo.co.in
Cc: Hans-Rudolf Hotz h...@fmi.ch; 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 me_shash...@yahoo.co.in
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 h...@fmi.ch
To: shashi shekhar me_shash...@yahoo.co.in
Cc: galaxy-dev@lists.bx.psu.edu 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
___
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[galaxy-dev] visulaization tool
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, 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 h...@fmi.ch To: shashi shekhar me_shash...@yahoo.co.in Cc: galaxy-dev@lists.bx.psu.edu 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 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 ross.laza...@gmail.com To: shashi shekhar me_shash...@yahoo.co.in Cc: Hans-Rudolf Hotz h...@fmi.ch; 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 me_shash...@yahoo.co.in 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 h...@fmi.ch To: shashi shekhar me_shash...@yahoo.co.in Cc: galaxy-dev@lists.bx.psu.edu 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 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 ross.laza...@gmail.com To: shashi shekhar me_shash...@yahoo.co.in Cc: Hans-Rudolf Hotz h...@fmi.ch; 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 me_shash...@yahoo.co.in 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 ross.laza...@gmail.com To: shashi shekhar me_shash...@yahoo.co.in Cc: Hans-Rudolf Hotz h...@fmi.ch; 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 me_shash...@yahoo.co.in 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 h...@fmi.ch To: shashi shekhar me_shash...@yahoo.co.in Cc: galaxy-dev@lists.bx.psu.edu 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 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 ross.laza...@gmail.com To: shashi shekhar me_shash...@yahoo.co.in Cc: galaxy-dev@lists.bx.psu.edu 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 me_shash...@yahoo.co.in 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 ross.laza...@gmail.com To: shashi shekhar me_shash...@yahoo.co.in Cc: Hans-Rudolf Hotz h...@fmi.ch; 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 me_shash...@yahoo.co.in 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 ross.laza...@gmail.com To: shashi shekhar me_shash...@yahoo.co.in Cc: Hans-Rudolf Hotz h...@fmi.ch; 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 me_shash...@yahoo.co.in 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 h...@fmi.ch To: shashi shekhar me_shash...@yahoo.co.in Cc: galaxy-dev@lists.bx.psu.edu 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
[galaxy-dev] trannsfer files from remote system to galaxy
Hi, In my local instance of Galaxy ,I want to add one option in which i can get files from remote system to galaxy in data library . except url is there any option to get remote files from galaxy ? Regards ___ 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/
[galaxy-dev] Regarding display application
Hi All.,
I need help in understanding the xml tag for display_application. i
don't know how all these xml tags works . can u provide me links for
understanding those tags like
target_frame
type=template
viewable=False
display id=genetrack_interval version=1.0.0 name=view in
link id=genetrack name=GeneTrack
url
target_frame=galaxy_mainhttp://genetrack.g2.bx.psu.edu/galaxy?filename=${encoded_filename.qp}amp;hashkey=${hash_key.qp}amp;input=${qp(str($genetrack_file.id))}amp;GALAXY_URL=${galaxy_url.qp}/url
param type=data name=bed_file viewable=False
format=bed6,genetrack/ !-- for now, we'll explicitly take care of
the multi-step conversion; walk genetrack datatype down as a
conversion of genetrack to genetrack doesn't exist and would likely be
pointless --
param type=data dataset=bed_file name=genetrack_file
format=genetrack viewable=False /
param type=template name=galaxy_url strip=True
${BASE_URL}/tool_runner?tool_id=predict2genetrack
/param
param type=template name=hash_key strip=True
#from galaxy.util.hash_util import hmac_new
${hmac_new( $APP.config.tool_secret, $genetrack_file.file_name )}
/param
param type=template name=encoded_filename strip=True
#import binascii
${binascii.hexlify( $genetrack_file.file_name )}
/param
/link
/display
Regards
shashi shekhar
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Re: [galaxy-dev] Regarding display application
On Tue, Sep 6, 2011 at 3:33 PM, shashi shekhar meshash...@gmail.com wrote:
Hi All.,
I need help in understanding the xml tag for display_application. i
don't know how all these xml tags works . can u provide me links for
understanding those tags like
target_frame
type=template
viewable=False
display id=genetrack_interval version=1.0.0 name=view in
link id=genetrack name=GeneTrack
url
target_frame=galaxy_mainhttp://genetrack.g2.bx.psu.edu/galaxy?filename=${encoded_filename.qp}amp;hashkey=${hash_key.qp}amp;input=${qp(str($genetrack_file.id))}amp;GALAXY_URL=${galaxy_url.qp}/url
param type=data name=bed_file viewable=False
format=bed6,genetrack/ !-- for now, we'll explicitly take care of
the multi-step conversion; walk genetrack datatype down as a
conversion of genetrack to genetrack doesn't exist and would likely be
pointless --
param type=data dataset=bed_file name=genetrack_file
format=genetrack viewable=False /
param type=template name=galaxy_url strip=True
${BASE_URL}/tool_runner?tool_id=predict2genetrack
/param
param type=template name=hash_key strip=True
#from galaxy.util.hash_util import hmac_new
${hmac_new( $APP.config.tool_secret, $genetrack_file.file_name )}
/param
param type=template name=encoded_filename strip=True
#import binascii
${binascii.hexlify( $genetrack_file.file_name )}
/param
/link
/display
Regards
shashi shekhar
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Re: [galaxy-dev] Regarding display application
Hi all,
Thanks for reply . I have an application to visualize some
custom datatyes inputs . i want to integrate this application with
galaxy . i have already added datatypes in my local instance of
Galaxy . Is It required to modify my application ?
Regards
shashi
On Tue, Sep 6, 2011 at 6:42 PM, Daniel Blankenberg d...@bx.psu.edu wrote:
Hi Shashi,
The docs for external display application could use some enhancement, but I
have provided details on the features you are asking about below.
target_frame: this is the frame where you want this external display
application to appear.
type=template: this parameter type is a cheetah template; like command
and configfile tags in tools
viewable=False: is this parameter viewable over http/s? When set to false,
you will be able to access and use the parameter in the generation of the
display applications, but it will not be accessible over the web via a URL.
GeneTrack accesses files directly over the filesystem, so the files do not
need to be web accessible for the display application.
Thanks for using Galaxy,
Dan
On Sep 6, 2011, at 6:03 AM, shashi shekhar wrote:
Hi All.,
I need help in understanding the xml tag for display_application. i
don't know how all these xml tags works . can u provide me links for
understanding those tags like
target_frame
type=template
viewable=False
display id=genetrack_interval version=1.0.0 name=view in
link id=genetrack name=GeneTrack
url
target_frame=galaxy_mainhttp://genetrack.g2.bx.psu.edu/galaxy?filename=${encoded_filename.qp}amp;hashkey=${hash_key.qp}amp;input=${qp(str($genetrack_file.id))}amp;GALAXY_URL=${galaxy_url.qp}/url
param type=data name=bed_file viewable=False
format=bed6,genetrack/ !-- for now, we'll explicitly take care of
the multi-step conversion; walk genetrack datatype down as a
conversion of genetrack to genetrack doesn't exist and would likely be
pointless --
param type=data dataset=bed_file name=genetrack_file
format=genetrack viewable=False /
param type=template name=galaxy_url strip=True
${BASE_URL}/tool_runner?tool_id=predict2genetrack
/param
param type=template name=hash_key strip=True
#from galaxy.util.hash_util import hmac_new
${hmac_new( $APP.config.tool_secret, $genetrack_file.file_name )}
/param
param type=template name=encoded_filename strip=True
#import binascii
${binascii.hexlify( $genetrack_file.file_name )}
/param
/link
/display
Regards
shashi shekhar
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___
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[galaxy-dev] adding display application in local instance of galaxy
Hi All ,
i am working in galaxy tool . i want to add one visualization tools
in galaxy . i don't understand how the display applications works .
tag ox xml file is not clear for display application .
can u just explain the meaning of type=template tag , target_frame
tag , amp tag ,BASE URL , strip tag and viewable tag in this xml?
display id=genetrack_interval version=1.0.0 name=view in
link id=genetrack name=GeneTrack
url
target_frame=galaxy_mainhttp://genetrack.g2.bx.psu.edu/galaxy?filename=${encoded_filename.qp}amp;hashkey=${hash_key.qp}amp;input=${qp(str($genetrack_file.id))}amp;GALAXY_URL=${galaxy_url.qp}/url
param type=data name=bed_file viewable=False
format=bed6,genetrack/ !-- for now, we'll explicitly take care of
the multi-step conversion; walk genetrack datatype down as a
conversion of genetrack to genetrack doesn't exist and would likely be
pointless --
param type=data dataset=bed_file name=genetrack_file
format=genetrack viewable=False /
param type=template name=galaxy_url strip=True
${BASE_URL}/tool_runner?tool_id=predict2genetrack
/param
param type=template name=hash_key strip=True
#from galaxy.util.hash_util import hmac_new
${hmac_new( $APP.config.tool_secret, $genetrack_file.file_name )}
/param
param type=template name=encoded_filename strip=True
#import binascii
${binascii.hexlify( $genetrack_file.file_name )}
/param
/link
/display
Regards
shashi shekhar
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[galaxy-dev] problem in workflow
Hi All, I am using local instance of galaxy,i am not able to use workflow .when i am clicking on workflow , it' displaying the loading picture only . i am not able to see workflow editor. may it depends on browser? 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/
[galaxy-dev] Problem with workflow
Hi, i am not able to create workflow in my local instance of galaxy. it's displaying only loading picture on browser. i am using old version version galaxy. Regards shashi shekhar ___ 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/
Re: [galaxy-dev] Problems with load_workflow_editor
No, it is happening only my instance of galaxy . i am using older version of galaxy . can it happen some browser won't support galaxy old version . On Sat, Sep 3, 2011 at 12:30 AM, Kanwei Li kan...@gmail.com wrote: Hi Shashi, Does this only happen on your instance or does it happen on our public instance as well? Thanks, K On Fri, Sep 2, 2011 at 6:46 AM, shashi shekhar meshash...@gmail.comwrote: Hi All, i am not able to create workflow in my local instance of galaxy. it's displaying only loading picture on browser when i am clicking on edit option of workflow . how can we resolve such type of problem ? i am using old version version galaxy. 192.168.60.115, 145.139.1.156 - - [02/Sep/2011:16:13:50 +0600] GET /workflow/get_datatypes?_=1314940546255 HTTP/1.1 200 - http://garu.ac.in/workflow/editor?id=df7a1f0c02a5b08e; Mozilla/5.0 (Windows; U; Windows NT 6.1; en-US; rv:1.9.2.17) Gecko/20110420 Firefox/3.6.17 192.168.60.115, 145.139.1.156 - - [02/Sep/2011:16:13:51 +0600] GET /workflow/load_workflow?_=1314940546462id=df7a1f0c02a5b08e_=true HTTP/1.1 200 - http://garu.ac.in/workflow/editor?id=df7a1f0c02a5b08e; Mozilla/5.0 (Windows; U; Windows NT 6.1; en-US; rv:1.9.2.17) Gecko/20110420 Firefox/3.6.17 Regards shashi shekhar ___ 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/ ___ 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/
[galaxy-dev] tool which using web service
hi, I have application , i want to integrate that application like ucsc_browser in my local instance of galaxy .Application create some input data ,that data i want to send into galaxy to process. can u help me how can i add such type of 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/
Re: [galaxy-dev] tool which using web service
i have an application ,from there i want input file in galaxy like usc_browser. in tools/data-source/ucsc_tablebrowser.xml u are passing some values from galaxy to ucsc_browser .and theen u are getting some info from ucsc browser. i want to crate tool like this. can i get any documents for such type of tool. thanks for reply On Wed, Aug 24, 2011 at 6:57 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hello Sashi, Look at our tool wikis at http://wiki.g2.bx.psu.edu/Admin/Tools You probably want to base your tool config file on ~/tools/data-source/ucsc_tablebrowser.xml. Greg Von kuster On Aug 24, 2011, at 9:12 AM, shashi shekhar wrote: hi, I have application , i want to integrate that application like ucsc_browser in my local instance of galaxy .Application create some input data ,that data i want to send into galaxy to process. can u help me how can i add such type of 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/ Greg Von Kuster Galaxy Development Team g...@bx.psu.edu ___ 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/
[galaxy-dev] visualization tool
Hi All, I want to add my own Visualization tool in local instance of galaxy .how i will do it in galaxy ? i want to integrate jmol 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/
Re: [galaxy-dev] visualization tool
Hi, In Galaxy there is visualization option .how it works .Are documents are available for visualization tool. Thanks for Reply Regards shashi On Tue, Aug 23, 2011 at 5:55 PM, Daniel Blankenberg d...@bx.psu.edu wrote: Hi Shashi, Have a look at: http://wiki.g2.bx.psu.edu/Admin/Tools/External%20Display%20Applications%20Tutorial And at the XML files in the directory: $GALAXY_ROOT/display_applications/ Thanks for using Galaxy, Dan On Aug 23, 2011, at 7:30 AM, shashi shekhar wrote: Hi All, I want to add my own Visualization tool in local instance of galaxy .how i will do it in galaxy ? i want to integrate jmol 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/ ___ 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/
Re: [galaxy-dev] visualization tool
On Tue, Aug 23, 2011 at 6:17 PM, shashi shekhar meshash...@gmail.comwrote: Hi, Iis it possible to add own visualization tool in galaxy? On Tue, Aug 23, 2011 at 5:55 PM, Daniel Blankenberg d...@bx.psu.eduwrote: Hi Shashi, Have a look at: http://wiki.g2.bx.psu.edu/Admin/Tools/External%20Display%20Applications%20Tutorial And at the XML files in the directory: $GALAXY_ROOT/display_applications/ Thanks for using Galaxy, Dan On Aug 23, 2011, at 7:30 AM, shashi shekhar wrote: Hi All, I want to add my own Visualization tool in local instance of galaxy .how i will do it in galaxy ? i want to integrate jmol 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/ ___ 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/
[galaxy-dev] How to get tool id in runner file (local.py)
Hi, I have local instance of Galaxy and i am doing some modification in Galaxy .So i need tool id id in local.py file . How i will get this information in runner file (local.py). Regards shashi shekhar ___ 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/
[galaxy-dev] Parallel job through galaxy
Hi All, I have local instance of Galaxy .I have system of very good configuration .it has many cores and I want to use multiprocessor for some tool. Have you added any tool which uses multiprocessor in Galaxy ? Provide me tool name . in my system pbs is installed . How can i use multiprocessor in Galaxy ? Regards shashi shekhar ___ 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/
[galaxy-dev] problem with job runner
Hi In my galaxy instance, whatever jobs i am submitting it goes into queued state. If I restart the server then the previous submitted jobs state changes to running. but the newly submitted jobs again goes to queued state. I am at a loss to understand this behaviour of galaxy and unable to debug it. The job submission uses a customized runner. How is it actually goes into the queued state automatically when all the workers thread are free? Does galaxy_session table is_valid attribute makes jobs state true? Or what all places in tables the queued states are getting stored. I can only see that the jobs table state attribute only stores the state. The server logs points error here: galaxy.jobs ERROR 2011-07-29 11:01:28,098 failure running job 2243 Traceback (most recent call last): File /home/gwadmin/galaxy-central/ lib/galaxy/jobs/__init__.py, line 202, in __monitor_step self.dispatcher.put( JobWrapper( job, self ) ) File /home/gwadmin/galaxy-central/lib/galaxy/jobs/__init__.py, line 856, in put self.job_runners[runner_name].put( job_wrapper ) File /home/gwadmin/galaxy-central/lib/galaxy/jobs/runners/gw.py, line 375, in put job_wrapper.change_state( model.Job.states.QUEUED ) File /home/gwadmin/galaxy-central/lib/galaxy/jobs/__init__.py, line 437, in change_state self.sa_session.flush() 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/
Re: [galaxy-dev] job runner error
Hi All, I have moved my database from sqlite to postgresql in my local instance of Galaxy .But I want my old history in new database.How It's possible ? Regards shashi On Wed, Jul 27, 2011 at 7:19 PM, Peter Cock p.j.a.c...@googlemail.comwrote: On Wed, Jul 27, 2011 at 2:14 PM, shashi shekhar meshash...@gmail.com Hi all, I have added separate job runner in my galaxy instance. So far it was running successfully from many months. Now its giving error as below and i am unable to trace it. Please suggest. Traceback (most recent call last): ... OperationalError: (OperationalError) database is locked None None Thanks Shashi On Wed, Jul 27, 2011 at 7:00 PM, Peter Cock p.j.a.c...@googlemail.com You're not using SQLite as the database are you? I've seen that kind of error message from locking problems (e.g. when the SQLite DB was on a CIFS mapped drive), and it wouldn't surprise me that with a separate thread for the job runner you get contention over the SQLite DB. If you are using PostgreSQL (or MySQL) as recommended for a production Galaxy server, then I'm not sure what could be wrong. On Wed, Jul 27, 2011 at 2:42 PM, shashi shekhar meshash...@gmail.com wrote: I am using sqlite database . I think that to avoid this database problem you will have to move to PostgreSQL (which is what the Galaxy team recommend), or possibly MySQL (not sure what the downsides are). This might be hard if you already have a number of users and datafiles. I've CC'd the list again so hopefully Nate or one of the other Galaxy Devs can confirm this. Peter ___ 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/
[galaxy-dev] job runner issue
Hi In my galaxy instance, whatever jobs i am submitting it goes into queued state. If I restart the server then the previous submitted jobs state changes to running. but the newly submitted jobs again goes to queued state. I am at a loss to understand this behaviour of galaxy and unable to debug it. The job submission uses a customized runner. How is it actually goes into the queued state automatically when all the workers thread are free? Does galaxy_session table is_valid attribute makes jobs state true? Or what all places in tables the queued states are getting stored. I can only see that the jobs table state attribute only stores the state. The server logs points error here: galaxy.jobs ERROR 2011-07-29 11:01:28,098 failure running job 2243 Traceback (most recent call last): File /home/gwadmin/galaxy-central/lib/galaxy/jobs/__init__.py, line 202, in __monitor_step self.dispatcher.put( JobWrapper( job, self ) ) File /home/gwadmin/galaxy-central/lib/galaxy/jobs/__init__.py, line 856, in put self.job_runners[runner_name].put( job_wrapper ) File /home/gwadmin/galaxy-central/lib/galaxy/jobs/runners/gw.py, line 375, in put job_wrapper.change_state( model.Job.states.QUEUED ) File /home/gwadmin/galaxy-central/lib/galaxy/jobs/__init__.py, line 437, in change_state self.sa_session.flush() Regards Karuna ___ 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/
[galaxy-dev] database problem
Hi ALL, I want to delete some data from history_dataset_association. Will it effect any other tables.and I want to delete records for last 3 days by sqlite query manually.How may tables will be effected by this and provide me tables name .How can i delete the records. Regards shashi shekhar ___ 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/
[galaxy-dev] job runner error
Hi all, I have added separate job runner in my galaxy instance. So far it was running successfully from many months. Now its giving error as below and i am unable to trace it. Please suggest. Traceback (most recent call last): File /home/gwadmin/galaxy-central/lib/galaxy/jobs/__init__.py, line 202, in __monitor_step self.dispatcher.put( JobWrapper( job, self ) ) File /home/gwadmin/galaxy-central/lib/galaxy/jobs/__init__.py, line 847, in put self.job_runners[runner_name].put( job_wrapper ) File /home/gwadmin/galaxy-central/lib/galaxy/jobs/runners/gw.py, line 370, in put job_wrapper.change_state( model.Job.states.QUEUED ) File /home/gwadmin/galaxy-central/lib/galaxy/jobs/__init__.py, line 428, in change_state self.sa_session.flush() File /home/gwadmin/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/scoping.py, line 127, in do return getattr(self.registry(), name)(*args, **kwargs) File /home/gwadmin/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/session.py, line 1356, in flush self._flush(objects) File /home/gwadmin/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/session.py, line 1438, in _flush transaction.commit() File /home/gwadmin/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/session.py, line 382, in commit t[1].commit() File /home/gwadmin/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/engine/base.py, line 1036, in commit self._do_commit() File /home/gwadmin/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/engine/base.py, line 1060, in _do_commit self.connection._commit_impl() File /home/gwadmin/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/engine/base.py, line 750, in _commit_impl self._handle_dbapi_exception(e, None, None, None, None) File /home/gwadmin/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/engine/base.py, line 931, in _handle_dbapi_exception raise exc.DBAPIError.instance(statement, parameters, e, connection_invalidated=is_disconnect) OperationalError: (OperationalError) database is locked None None Thanks 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/
[galaxy-dev] Fwd: Status of Job after log out
-- Forwarded message -- From: shashi shekhar meshash...@gmail.com Date: Tue, Jul 19, 2011 at 3:41 PM Subject: Status of Job after log out To: shashi shekhar meshash...@gmail.com Hi all, I took one job which takes long time to run . In galaxy, this job was submitted . After log out from galaxy ,job was running . After login again ,i checked the status of job . It showed running . How is it implemented in galaxy ? Regards shashi shekhar ___ 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/
[galaxy-dev] Using the tool after log in
Hi All, I have local instance of galaxy . I want to make changes in such a way that after log in, user should able to submit any job or run any tool. Log in should be compulsory to run any tool including upload tool. Whenever someone clicks on tool without log in ,it should display message like You must be logged in http://192.168.62.51:8089/user/login?webapp=galaxy to use Galaxy . Reagrds shashi shekhar ___ 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/
[galaxy-dev] Regarding output file name in download option
Hi All, it's possible to give output file name in tool xml .while downloading same output file name should come. i don't want to change the extension . Regards shashi shekhar ___ 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/
[galaxy-dev] Regarding output file name in save option of history
Hi All, it's possible to give output file name in tool xml and while downloading same output file name should come. i don't want to change the extension .output file name should not start with Galaxy word . Regards shashi shekhar ___ 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/
[galaxy-dev] Regarding saving the file
Hi All,
a href=${h.url_for( controller='dataset', action='display',
dataset_id=dataset_id, to_ext=data.ext )} title=Save class=icon-button
disk tooltip/a
Can u tell me how it works?.when u click on save button, it will save a file
as output file name appended with extension example
Galaxy122-[fasta-compute-sequence-length].fasta . i want to remove the first
word Galaxy. how it's possible ?
Regards
shashi shekhar
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[galaxy-dev] stdout and stderr while using pbs
Hi All, if i am using pbs . in this i am getting stderror and stdout . then how can i handle such type of problem. can i check the standard error before displaying anything on browser. Reagrds shashi shekhar ___ 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/
[galaxy-dev] stdout and stderr
Hi all, I am using one tool which gives stdout and stderr . it is showing red color (job failed) in browser.How can i resolve such type of problem. Regards shashi shekhar ___ 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/
[galaxy-dev] Problem with file's extension
Hi All, I have some problem with extension of file.some executables file will recognize the only the specific extension like autodock . it takes one input file ( extension with .dpf ) and one outpt file (extension with .dlg). how can we resolve such type of problem . Regards Shashi shekhar ___ 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/
[galaxy-dev] requirement of complete command in code file
Hi All, I am doing some changes in galaxy software . I need the complete command in code file .is it possible ? if it's possible,provide me the code for that . Reagrds shashi shekhar ___ 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/
[galaxy-dev] Problem fore getting tool Command in code file
Hi All, I need the tool command in code file and want to change the command . is there any way to change the command which is given under command tag . Reagrds shashi shekhar ___ 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/
[galaxy-dev] galaxy related
if i want some in information from tool xml file to code file ,how i will get the info. it it's possible ,send me detailed info. Regards galaxy user shashi shekhar ___ 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/
