thanks

----- Original Message -----
From: rbrown1422@comcast.net
To: galaxy-dev <galaxy-dev@lists.galaxyproject.org>
Sent: Thu, 04 Feb 2016 19:05:06 -0000 (UTC)
Subject: Fwd: Rscript run under Tools Directory cannot see Datafile in History smaller email size

Good morning team,

I have an Rscript tool that is trying to read a file I uploaded into the history beforehand.  Galaxy is running with the same user and privileges as the dataset directory.

    <command>Rscript --slave --vanilla --file=$GALAXY_ROOT_DIR/tools/Foo/Foo.R --args $inputFile1 ..... </command>

Why would this be?

Error in file(file, "rt") : cannot open the connection
Calls: performDataOrdering -> read.table -> file
In addition: Warning message:
In file(file, "rt") :
  cannot open file '--file=/home/rbrown/hmgalaxy/database/files/000/dataset_162.dat': No such file or directory
Execution halted

When I try to run as R versus Rscript - I get a syntax error about unexpected '(' on function call that works fine in R window.

Thanks
Bob