----- Original Message -----From: email@example.comTo: galaxy-dev
<firstname.lastname@example.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
<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.
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