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)
See some very important Gscope Procedures
- 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
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