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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 how to access our postgresql, mysql and sqlite databases

Gscope Documentatiopn Project (from Benjamin Linard)


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
  • 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