Forgot to cc the mailing list. -John On Thu, Feb 4, 2016 at 8:11 PM, John Chilton <jmchilton@gmail.com> wrote:
Are you sure about the --file when calling Rscript?
Here is the usage for my local version which does not expect an argument named --file:
Usage: /path/to/Rscript [--options] [-e expr] file [args]
--options accepted are --help Print usage and exit --version Print version and exit --verbose Print information on progress --default-packages=list Where 'list' is a comma-separated set of package names, or 'NULL' or options to R, in addition to --slave --no-restore, such as --save Do save workspace at the end of the session --no-environ Don't read the site and user environment files --no-site-file Don't read the site-wide Rprofile --no-init-file Don't read the user R profile --restore Do restore previously saved objects at startup --vanilla Combine --no-save, --no-restore, --no-site-file --no-init-file and --no-environ
'file' may contain spaces but not shell metacharacters
Also, instead of using $GALAXY_ROOT - I would use $__tool_directory__ if the tool XML file is located next to the RScript, like this:
$__tool_directory__/Foo.R
-John
On Thu, Feb 4, 2016 at 7:05 PM, <rbrown1422@comcast.net> wrote:
Good morning team, I have an Rscript tool that is trying to read a file I uploaded into the history beforehand. Galaxy is running with the same user and privileges as the dataset directory. <command>Rscript --slave --vanilla --file=$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
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