[galaxy-dev] galaxy related

2011-03-31 Thread shashi shekhar
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

[galaxy-dev] Fwd: Your message to galaxy-dev awaits moderator approval

2011-05-23 Thread shashi shekhar
-- Forwarded message -- From: galaxy-dev-boun...@lists.bx.psu.edu 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

[galaxy-dev] requirement of complete command in code file

2011-05-23 Thread shashi shekhar
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

[galaxy-dev] Problem fore getting tool Command in code file

2011-05-23 Thread shashi shekhar
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

[galaxy-dev] Problem with file's extension

2011-05-25 Thread shashi shekhar
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

[galaxy-dev] stdout and stderr

2011-05-26 Thread shashi shekhar
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

[galaxy-dev] stdout and stderr while using pbs

2011-05-27 Thread shashi shekhar
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

[galaxy-dev] Regarding output file name in download option

2011-06-28 Thread shashi shekhar
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

[galaxy-dev] Regarding output file name in save option of history

2011-06-28 Thread shashi shekhar
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

[galaxy-dev] Regarding saving the file

2011-06-28 Thread shashi shekhar
-[fasta-compute-sequence-length].fasta . i want to remove the first word Galaxy. how it's possible ? Regards shashi shekhar ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions

[galaxy-dev] Using the tool after log in

2011-06-30 Thread shashi shekhar
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-dev] how to reduce Load of galaxy in standalone system by python

2011-07-07 Thread shashi shekhar
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 ___ Please keep all

[galaxy-dev] Fwd: Status of Job after log out

2011-07-19 Thread shashi shekhar
-- 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

[galaxy-dev] database problem

2011-07-27 Thread shashi shekhar
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

[galaxy-dev] job runner error

2011-07-27 Thread 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,

Re: [galaxy-dev] job runner error

2011-07-28 Thread shashi shekhar
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

[galaxy-dev] job runner issue

2011-07-28 Thread shashi shekhar
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

[galaxy-dev] problem with job runner

2011-07-29 Thread shashi shekhar
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

[galaxy-dev] How to get tool id in runner file (local.py)

2011-08-16 Thread shashi shekhar
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

[galaxy-dev] Parallel job through galaxy

2011-08-16 Thread shashi shekhar
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/

Re: [galaxy-dev] Parallel job through galaxy

2011-08-16 Thread shashi shekhar
On Tue, Aug 16, 2011 at 3:46 PM, Peter Cock p.j.a.c...@googlemail.comwrote: On Tue, Aug 16, 2011 at 11:13 AM, shashi shekhar meshash...@gmail.com 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

[galaxy-dev] visualization tool

2011-08-23 Thread shashi shekhar
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

Re: [galaxy-dev] visualization tool

2011-08-23 Thread shashi shekhar
/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

Re: [galaxy-dev] visualization tool

2011-08-23 Thread shashi shekhar
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

Re: [galaxy-dev] How to get tool id in runner file (local.py)

2011-08-23 Thread shashi shekhar
thanks for reply. On Wed, Aug 24, 2011 at 3:32 AM, Nate Coraor n...@bx.psu.edu 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 information in runner

[galaxy-dev] tool which using web service

2011-08-24 Thread shashi shekhar
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

Re: [galaxy-dev] tool which using web service

2011-08-24 Thread shashi shekhar
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

[galaxy-dev] problem in workflow

2011-09-02 Thread shashi shekhar
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

[galaxy-dev] Problem with workflow

2011-09-02 Thread shashi shekhar
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

Re: [galaxy-dev] Problems with load_workflow_editor

2011-09-02 Thread shashi shekhar
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

[galaxy-dev] adding display application in local instance of galaxy

2011-09-05 Thread shashi shekhar
)} /param /link /display 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

[galaxy-dev] Regarding display application

2011-09-06 Thread shashi shekhar
, $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

Re: [galaxy-dev] Regarding display application

2011-09-06 Thread shashi shekhar
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

Re: [galaxy-dev] Regarding display application

2011-09-06 Thread shashi shekhar
, 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

[galaxy-dev] trannsfer files from remote system to galaxy

2011-09-08 Thread shashi shekhar
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

[galaxy-dev] visulaization tool

2013-06-19 Thread shashi shekhar
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

Re: [galaxy-dev] visulaization tool

2013-06-19 Thread shashi shekhar
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

Re: [galaxy-dev] visulaization tool

2013-06-19 Thread shashi shekhar
, 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

Re: [galaxy-dev] visulaization tool

2013-06-19 Thread shashi shekhar
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

Re: [galaxy-dev] visulaization tool

2013-06-19 Thread shashi shekhar
= [            ]     # 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

Re: [galaxy-dev] visulaization tool

2013-06-20 Thread shashi shekhar
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

Re: [galaxy-dev] visulaization tool

2013-06-20 Thread shashi shekhar
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

Re: [galaxy-dev] visulaization tool

2013-06-21 Thread shashi shekhar
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

[galaxy-dev] How to enable auto option for newly added file formats

2013-06-24 Thread shashi shekhar
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

Re: [galaxy-dev] How to enable auto option for newly added file formats

2013-06-25 Thread shashi shekhar
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

Re: [galaxy-dev] How to enable auto option for newly added file formats

2013-06-25 Thread shashi shekhar
) 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

2013-06-26 Thread shashi shekhar
Hi Bjorn , thanks for reply ...my problem has solved ...it's working now .. regards shashi 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

[galaxy-dev] Extra authentication

2013-06-27 Thread shashi shekhar
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