Difference between revisions of "Gscope Environment Variables"
(New page: Gscope needs to now the Gscope Project it has to manage. For that folllowing environment variables are set with the command (see the file [http://www-bio3d-igbmc.u-strasbg.fr/Pou...) |
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| − | [[Gscope]] needs to | + | [[Gscope]] needs to know the [[Gscope Project]] it has to manage. |
For that folllowing environment variables are set with the command | For that folllowing environment variables are set with the command | ||
| − | (see the file [http://www-bio3d-igbmc.u-strasbg.fr/PourGscope/ | + | (see the file [http://www-bio3d-igbmc.u-strasbg.fr/~ripp/PourGscope/setgscope.com setgscope]) |
setgscoperr ''MyProject'' | setgscoperr ''MyProject'' | ||
| − | * setenv REPERTOIREDUGENOME /genomics/MyProject (the directory which contains the Gscope Project) | + | * setenv '''REPERTOIREDUGENOME''' /genomics/MyProject (the directory which contains the Gscope Project) |
* setenv NCBI /bips/share/ncbi | * setenv NCBI /bips/share/ncbi | ||
* setenv BLASTDB /catalog/blast | * setenv BLASTDB /catalog/blast | ||
| − | * the PATH is modified and contains at least | + | * the '''PATH''' is modified and contains at least |
** /home/ripp/gscope/bin | ** /home/ripp/gscope/bin | ||
** /home/ripp/mulali | ** /home/ripp/mulali | ||
| Line 23: | Line 23: | ||
setncbi | setncbi | ||
| − | REPERTOIREDUGENOME and home/ripp/gscope/bin are sufficient to run Gscope | + | '''REPERTOIREDUGENOME''' and '''/home/ripp/gscope/bin''' are necessary and sufficient to run Gscope in visualisation mode. |
| − | Please see the file [http://www-bio3d-igbmc.u-strasbg.fr/PourGscope/ | + | Please see the file [http://www-bio3d-igbmc.u-strasbg.fr/~ripp/PourGscope/setgscope.com setgscope] |
Latest revision as of 11:22, 16 April 2009
Gscope needs to know the Gscope Project it has to manage.
For that folllowing environment variables are set with the command (see the file setgscope)
setgscoperr MyProject
- setenv REPERTOIREDUGENOME /genomics/MyProject (the directory which contains the Gscope Project)
- setenv NCBI /bips/share/ncbi
- setenv BLASTDB /catalog/blast
- the PATH is modified and contains at least
- /home/ripp/gscope/bin
- /home/ripp/mulali
- /bips/EMBOSS/bin
- /bips/bin
Following command are also launched
setsrs setmulali setncbi
REPERTOIREDUGENOME and /home/ripp/gscope/bin are necessary and sufficient to run Gscope in visualisation mode.
Please see the file setgscope
