Rscript run under Tools Directory cannot see Datafile in History
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 $inputFile1 ..... </command> Why would this be? Error in file(file, "rt") : cannot open the connectionCalls: performDataOrdering -> read.table -> fileIn addition: Warning message:In file(file, "rt") : cannot open file '--file=/home/rbrown/hmgalaxy/database/files/000/dataset_162.dat': No such file or directoryExecution haltedWhen I try to run as R versus Rscript - I get a syntax error about unexpected '(' on function call that works fine in R window.ThanksBob
Good morning team, I have an Rscript tool that is trying to read a file I uploaded into the history beforehand. Galaxy is running with the same user and privileges as the dataset directory. <command>Rscript --slave --vanilla --file=$GALAXY_ROOT_DIR/tools/Foo/Foo.R --args $inputFile1 ..... </command> Why would this be? Error in file(file, "rt") : cannot open the connectionCalls: performDataOrdering -> read.table -> fileIn addition: Warning message:In file(file, "rt") : cannot open file '--file=/home/rbrown/hmgalaxy/database/files/000/dataset_162.dat': No such file or directoryExecution halted When I try to run as R versus Rscript - I get a syntax error about unexpected '(' on function call that works fine in R window. ThanksBob
thanks ----- Original Message -----From: rbrown1422@comcast.netTo: galaxy-dev <galaxy-dev@lists.galaxyproject.org>Sent: Thu, 04 Feb 2016 19:05:06 -0000 (UTC)Subject: Fwd: Rscript run under Tools Directory cannot see Datafile in History smaller email size Good morning team, I have an Rscript tool that is trying to read a file I uploaded into the history beforehand. Galaxy is running with the same user and privileges as the dataset directory. <command>Rscript --slave --vanilla --file=$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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