Gscope

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)

• Please visit also the private Wiki Gscope Documentation Project

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

• If the project already exists the Gscope Environment Variables are set.
• If it concerns a new project the directories are created and the variables are set. (see New Gscope Project)

• 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

• Gscope Clonage to design, order and manage oligos for Structural Genomics, it's a first step to a LIMS

How it works

• Main Architecture of Gscope