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
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Hi Bjorn ,
thanks for reply ...my problem has solved ...it's working now ..
regards
shashi
From: Björn Grüning
To: shashi shekhar
Cc: Peter Cock ; Galaxy Dev
Sent: Tuesday, 25 June 2013 9:44 PM
Subject: Re: [galaxy-dev] How to enable auto optio
) in data.py file ..
Regards
shahsi
From: Björn Grüning
To: shashi shekhar
Cc: Peter Cock ; Galaxy Dev
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
From: Peter Cock
To: shashi shekhar
Cc: Galaxy Dev
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 wrote:
> Hi,
>
> yeah ..i
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
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in y
contains only html tags ..not the actual content .
it wont's display the actual contents.
Regards
shashi
From: James Taylor
To: shashi shekhar
Cc: "galaxy-dev@lists.bx.psu.edu"
Sent: Thursday, 20 June 2013 8:57 PM
Subject: Re: [galaxy-dev
=${bed_file.qp}
what is the meaninng
and what is the use of url="galaxy.bed" ?
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] visulaizat
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 sh
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 J
em
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.
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.
AFAI
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&quo
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,
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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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
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Hi,
In my local instance of Galaxy ,I want to make change in "upload
files from file system" option which is used admin. in which file i
have to make changes ? i want to attach some more features in that.
Regards
shashi
___
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neration 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 Tue, Sep 6, 2011 at 3:33 PM, 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
>
&
hmac_new
${hmac_new( $APP.config.tool_secret, $genetrack_file.file_name )}
#import binascii
${binascii.hexlify( $genetrack_file.file_name )}
Regards
shashi shekhar
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me )}
Regards
shashi shekhar
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on our public
> instance as well?
>
> Thanks,
>
> K
>
> On Fri, Sep 2, 2011 at 6:46 AM, shashi shekhar wrote:
>
>> 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
- [02/Sep/2011:16:13:51 +0600] "GET
/workflow/load_workflow?_=1314940546462&id=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; r
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
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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
nitial
> response.
>
> http://wiki.g2.bx.psu.edu/Admin/Internals/Data%20Sources
>
>
> On Aug 24, 2011, at 12:15 PM, Greg Von Kuster wrote:
>
> Hello Shashi,
> On Aug 24, 2011, at 11:55 AM, shashi shekhar wrote:
>
> i have an application ,from there i want input file in
gt;
> 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
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
thanks for reply.
On Wed, Aug 24, 2011 at 3:32 AM, Nate Coraor wrote:
> shashi shekhar wrote:
> > 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
>
On Tue, Aug 23, 2011 at 6:17 PM, shashi shekhar wrote:
> Hi,
>
>
> Iis it possible to add own visualization tool in galaxy?
>
>
>
>
> On Tue, Aug 23, 2011 at 5:55 PM, Daniel Blankenberg wrote:
>
>> Hi Shashi,
>>
>> Have a look at:
>> ht
ols/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,
> >
> >
>
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
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On Tue, Aug 16, 2011 at 3:46 PM, Peter Cock wrote:
> On Tue, Aug 16, 2011 at 11:13 AM, shashi shekhar
> wrote:
> > Thanks Peter for reply
> > But i want to use galaxy for parallel programs like mpi and opemp .will
> it
> > support ?how can i configure for parallel p
multiprocessor in Galaxy ?
Regards
shashi shekhar
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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
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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 debu
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 debu
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 wrote:
> On Wed, Jul 27, 2011 at 2:14 PM, shashi shekhar
>
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",
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
-- Forwarded message --
From: shashi shekhar
Date: Tue, Jul 19, 2011 at 3:41 PM
Subject: Status of Job after log out
To: shashi shekhar
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
Hi All,
i have system with single cpu . and have installed galaxy .while running
galaxy it will create high load on system.
how are you reducing the load of galaxy in system by using the python .
Regards
shashi
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like "You
must be logged in <http://192.168.62.51:8089/user/login?webapp=galaxy> to
use Galaxy" .
Reagrds
shashi shekhar
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Hi All,
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
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 .
Re
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
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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
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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
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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
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Hi All,
I am using standalone system for galaxy and am doing some modification
in galaxy .i need the all output file names in local.py .How can i get all
the output file names in local.py file.
Regards
shashi shekhar
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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
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
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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
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-- Forwarded message --
From:
Date: Mon, May 23, 2011 at 11:42 AM
Subject: Your message to galaxy-dev awaits moderator approval
To: meshash...@gmail.com
Your mail to 'galaxy-dev' with the subject
requirement of complete command in code file
Is being held until the list moder
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
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