Difference between revisions of "Gscope Environment Variables"

From Wikili
Jump to: navigation, search
 
(One intermediate revision by the same user not shown)
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/~ripp/PourGscope/setgscope.com setgscope]
 
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