thanks

----- Original Message -----From: rbrown1422@comcast.netTo: 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 connectionCalls: 
performDataOrdering -> read.table -> fileIn addition: Warning message:In 
file(file, "rt") :  cannot open file 
'--file=/home/rbrown/hmgalaxy/database/files/000/dataset_162.dat': No such file 
or directoryExecution 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.

ThanksBob


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