Difference between revisions of "Gscope"
| Line 18: | Line 18: | ||
* [[GscopeSql]] how to access our postgresql and mysql databases | * [[GscopeSql]] how to access our postgresql and mysql databases | ||
==Usage== | ==Usage== | ||
| + | ===Normal usage with setgscoperr=== | ||
* Gscope works on a [[Gscope Project]] (a complete genome, a set of proteins, a set of genes, etc.) | * 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. | ||
| Line 26: | Line 27: | ||
* If the project already exists the [[Gscope Environment Variables]] are set. | * 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]]) | * If it concerns a new project the directories are created and the variables are set. (see [[New Gscope Project]]) | ||
| − | + | ===You can run gscope without setgscoperr=== | |
| + | Since 2010/08/26 it is possible to run directly gscope | ||
| + | |||
| + | gscope -project YouProject puts Command arg1 arg2 arg3 | ||
| + | |||
| + | and if you are shure not to use Tk | ||
| + | |||
| + | gscope -project YouProject -notk puts Command arg1 arg2 arg3 | ||
| + | |||
==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 | ||
Revision as of 17:53, 26 August 2010
New : Gscope knows a lot about GeneNames
Please visit also the private Wiki Gscope Documentation Project
Contents
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
- Please visit also the private Wiki Gscope Documentation Project
- Gscope Procedures
- GscopeSql how to access our postgresql and mysql databases
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 run gscope without setgscoperr
Since 2010/08/26 it is possible to run directly gscope
gscope -project YouProject puts Command arg1 arg2 arg3
and if you are shure not to use Tk
gscope -project YouProject -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
