Difference between revisions of "Gscope"
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| + | Please visit also the private wiki Lbgiki [http://lbgi.igbmc.fr/lbgiki/index.php/Gscope Gscope] | ||
==What is Gscope ?== | ==What is Gscope ?== | ||
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* Gscope is an integrated platform allowing the analysis of all kind of genomic data. | * 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 written in Tcl/Tk and runs on all systems. | ||
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* it allows also | * it allows also | ||
** the creation and feeding of SQL relational databases | ** the creation and feeding of SQL relational databases | ||
| − | ** the quering and display of the available information through a web based interface | + | ** the quering and display of the available information through a web based interface ([http://www-bio3d-igbmc.u-strasbg.fr/~ripp/cgi-bin/gsceop_html_server.tcsh 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 [http://lbgi.fr/lbgiki/index.php/GDP Gscope Documentation Project] | ||
==Usage== | ==Usage== | ||
| − | * Gscope works on a [[Gscope 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. | * To run Gscope you need to define the corresponding project. | ||
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gscope | gscope | ||
| − | * If the project already exists the [[Gscope Environment Variables]] are | + | * If the project already exists the [[Gscope Environment Variables]] are set. |
| − | * If it concerns a new project the directories are created and | + | * If it concerns a new project the directories are created and the variables are set. (see [[New Gscope Project]]) |
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| + | * You '''can execute any procedure''' of Gscope as command line '''*** THE BIGGEST IDEA I HAD ***''' | ||
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| + | 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 | ||
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| + | gscope yes ProcToExecute Arg1 Arg2 Arg3 #rR doen't ask any question using the default response and runs in batch mode | ||
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| + | * if you want to run Gscope in batch mode (as for example BlastPPourTous) | ||
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| + | 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 | ||
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| + | and if you are shure not to use Tk | ||
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| + | /home/ripp/gscope/bin/gscope -project ''MyProject'' '''-notk''' puts Command arg1 arg2 arg3 | ||
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==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 | ||
Latest revision as of 13:06, 27 January 2018
Please visit also the private wiki Lbgiki Gscope
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
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
