Difference between revisions of "Gscope"

Revision as of 14:44, 1 July 2014

New : Gscope knows a lot about GeneNames

Please visit also the private Wiki Gscope Documentation Project

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 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)

 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)

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

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

@@ Line 45: / Line 45: @@
 and if you are shure not to use Tk
-  gscope -project ''MyProject'' '''-notk''' puts Command arg1 arg2 arg3
+  /home/ripp/gscope/bin/gscope -project ''MyProject'' '''-notk''' puts Command arg1 arg2 arg3
 ==Gscope has some specific applications==