Difference between revisions of "Gscope"

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(Normal usage with setgscoperr)
 
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Please visit also the private wiki Lbgiki [http://lbgi.igbmc.fr/lbgiki/index.php/Gscope Gscope]
 
==What is Gscope ?==
 
==What is Gscope ?==
 
  New : Gscope knows a lot about [[GeneNames]]
 
 
 
* Gscope is an integrated platform allowing the analysis of all kind of genomic data.
 
* Gscope is an integrated platform allowing the analysis of all kind of genomic data.
 
* Gscope is written in Tcl/Tk and runs on all systems.
 
* Gscope is written in Tcl/Tk and runs on all systems.
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* it allows also
 
* it allows also
 
** the creation and feeding of SQL relational databases
 
** the creation and feeding of SQL relational databases
** the quering and display of the available information through a web based interface
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** the quering and display of the available information through a web based interface ([http://www-bio3d-igbmc.u-strasbg.fr/~ripp/cgi-bin/gsceop_html_server.tcsh Wscope])
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==Gscope Documentation==
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===Gscope Procedures===
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See some very important [[Gscope Procedures]]
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===GscopeSql===
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* [[GscopeSql]]  how to access our postgresql, mysql and sqlite databases
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===Gscope Documentatiopn Project (from Benjamin Linard)===
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* Please visit also the private Wiki [http://lbgi.fr/lbgiki/index.php/GDP Gscope Documentation Project]
  
 
==Usage==
 
==Usage==
* Gscope works on a [[Gscope Project]]
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===Normal usage with setgscoperr===
* A gscope Project can be a complete genome, a set of proteins, a set of genes, etc.  
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* Gscope works on a [[Gscope Project]] (a complete genome, a set of proteins, a set of genes, etc.)
 
* To run Gscope you need to define the corresponding project.
 
* To run Gscope you need to define the corresponding project.
  
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   gscope
 
   gscope
  
* If the project already exists the [[Gscope Environment Variables]] are setted.
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* If the project already exists the [[Gscope Environment Variables]] are set.
* If it concerns a new project the directories are created and th evariables are setted. (see [[New Gscope Project]])
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* If it concerns a new project the directories are created and the variables are set. (see [[New Gscope Project]])
   
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* You '''can execute any procedure''' of Gscope as command line  '''*** THE BIGGEST IDEA I HAD ***'''
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  gscope puts ProcToExecute Arg1 Arg2 Arg3      #rR executes ProcToExecute, displays the result and stops
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  gscope putl ProcToExecute Arg1 Arg2 Arg3      #rR executes ProcToExecute, displays the result joining all elements of the list with \n and stops
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  gscope exe ProcToExecute Arg1 Arg2 Arg3      #rR executes ProcToExecute and stops
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  gscope putsandcontinue ProcToExecute Arg1 ... #rR same as before but doesn't stop
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  gscope yes ProcToExecute Arg1 Arg2 Arg3      #rR doen't ask any question using the default response and runs in batch mode
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* if you want to run Gscope in batch mode (as for example BlastPPourTous)
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 +
  glance BlastPPourTous
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  glance BlastPPourTous 8
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  glance "BlastPPourTous All /blast/uniref90" 12
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if the command is more then one word you have to use " "
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the last number says how many process to run simultaneously (4 by default)
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 +
===You can run gscope without setgscoperr===
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Since 2010/08/26 it is possible to run directly gscope
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/home/ripp/gscope/bin/gscope '''-project''' ''MyProject'' puts Command arg1 arg2 arg3
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and if you are shure not to use Tk
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/home/ripp/gscope/bin/gscope -project ''MyProject'' '''-notk''' puts Command arg1 arg2 arg3
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==Gscope has some specific applications==
 
==Gscope has some specific applications==
 
* [[Gscope Clonage]] to design, order and manage oligos for [[Structural Genomics]], it's a first step to a LIMS
 
* [[Gscope Clonage]] to design, order and manage oligos for [[Structural Genomics]], it's a first step to a LIMS

Latest revision as of 12:06, 27 January 2018

Please visit also the private wiki Lbgiki Gscope

What is Gscope ?

  • Gscope is an integrated platform allowing the analysis of all kind of genomic data.
  • Gscope is written in Tcl/Tk and runs on all systems.
  • Gscope is specially designed to perform high throughput analysis.
  • Gscope is mainly composed of
    • all tools necessary to create the basic data
    • analysis tools
    • visualisation interface
  • it allows also
    • the creation and feeding of SQL relational databases
    • the quering and display of the available information through a web based interface (Wscope)

Gscope Documentation

Gscope Procedures

See some very important Gscope Procedures

GscopeSql

  • GscopeSql how to access our postgresql, mysql and sqlite databases

Gscope Documentatiopn Project (from Benjamin Linard)

Usage

Normal usage with setgscoperr

  • Gscope works on a Gscope Project (a complete genome, a set of proteins, a set of genes, etc.)
  • To run Gscope you need to define the corresponding project.
 setgscoperr MyProject
 gscope
  • You can execute any procedure of Gscope as command line *** THE BIGGEST IDEA I HAD ***
  gscope puts ProcToExecute Arg1 Arg2 Arg3      #rR executes ProcToExecute, displays the result and stops
  gscope putl ProcToExecute Arg1 Arg2 Arg3      #rR executes ProcToExecute, displays the result joining all elements of the list with \n and stops
  gscope exe  ProcToExecute Arg1 Arg2 Arg3      #rR executes ProcToExecute and stops
  gscope putsandcontinue ProcToExecute Arg1 ... #rR same as before but doesn't stop
  gscope yes ProcToExecute Arg1 Arg2 Arg3       #rR doen't ask any question using the default response and runs in batch mode
  • if you want to run Gscope in batch mode (as for example BlastPPourTous)
 glance BlastPPourTous
 glance BlastPPourTous 8
 glance "BlastPPourTous All /blast/uniref90" 12

if the command is more then one word you have to use " " the last number says how many process to run simultaneously (4 by default)

You can run gscope without setgscoperr

Since 2010/08/26 it is possible to run directly gscope

/home/ripp/gscope/bin/gscope -project MyProject puts Command arg1 arg2 arg3

and if you are shure not to use Tk

/home/ripp/gscope/bin/gscope -project MyProject -notk puts Command arg1 arg2 arg3

Gscope has some specific applications

How it works