defining an application with SRS6

Rene Heek heek at zib.de
Sat Aug 10 05:16:44 EST 2002


hi,

i've tried to setup a not predefined apllication in srs6, but failed
somehow. the documentation isn't very helpful (for me), maybe someone
can help me.

the apllication (they called it 'wessel') has no parameter in this stage
of development, so i reduced my AppOpp-set to jobName_option. this works
fine right now, the application is launched, produces some output-files,
which are copied back from where the application was launched. then srs
indices this file (temp_job1.<appname>) correctly (i can acces the
results via database selection in srs6). but srs doens't show me the
result right after executing my app ? when starting the indexscript
(temp_<appname>_1_index.csh) manually it says: 'error: databank has no
active read links, "WESSEL'. maybe the links are wrong:), but how do i
define them corractly ?

btw. has someone a idea how to get the $pwd variable, instead of
($Env:SRSROOT)/tmp/($ParStr:userId), in commandWrapper ? it works, but
this doesn't look very elegant to me. i've tried ($Env:PWD) but this
won't work on my machine.

thanks a lot 

rene heek

here my definitions:
wessel.i

#
# almost like genbank ...
#

$WESSEL_DB=$Library:[WESSEL group:$APPLICATION_LIBS 
  printName:'Wessel Results'
  parallelType:filesSize partSizeKb:200000 
  defaultView:$Entries_View
  defaultEntryView:$GenbankEntry_View
  entryViews:{$Entries_View $GenbankEntry_View}
  format:$GENBANK_FORMAT cachesize:512 maxNameLen:16 type:user
  searchName:'*.wessel'
  links:{
    $Link:[$WESSEL_DB to:$GENBANKREL_DB     fromField:$DF_Accession 
toField:$DF_Accession weight:11]
  }
]

#
#
#

$WESSEL_APP=$Application:[Wessel
  launchFromTopPage:y
  title:'a tool to wessel' 
  resultDb:$WESSEL_DB
  options:{
    $jobName_Option
  }

  command: @{
    $opt.command = 
       |longcomp ($Env:SRSROOT)/tmp/($ParStr:userId) ($appl.outFile)
  }

  commandWrapper: @{
     |($opt.command)
     |echo 'ready'

  }

  comment:
          | a very wessel application.

]





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