User: Bree, Freddy de

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Posts by Bree, Freddy de

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Listing Attributes Of Data Input
... Dear all, I was wondering if there is a place within the Galaxy content (a config, an xml file) that gives me some handles on how to address attributes of data input. For example, I can get the 'file_name' of data input, by addressing this attr as 'input.file_name', and for example, the original n ...
galaxy written 6.9 years ago by Bree, Freddy de80 • updated 6.9 years ago by Peter260
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Answer: A: Plugging R Into Galaxy
... The out.data is simply picked up by galaxy: As long as you define your variable capturing the output and also in your tool.xml file. Make sure the output is defined as "data" in the tool.xml file. Initially I thought the same thing, but the piping is not needed with '>', worse, it doesn't work ...
written 7.1 years ago by Bree, Freddy de80
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Answer: A: Re: Galaxy-User Digest, Vol 26, Issue 6
... Hi Anthony, You can avoid working with wrappers to run 3 scripts (your R-script, a perl or shell wrapper and the necessary xml file) to make 1 actually run what you want to do. I've struggled with this in the previous digests, which are not so accessible to search-find. simply put in your tool.xm ...
written 7.1 years ago by Bree, Freddy de80
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Answer: A: Running R In Galaxy
... Following the discussion on this topic, the solution: You can run R 'straight' in galaxy without a wrapper: R --slave --vanilla --file=$GALAXY_ROOT_DIR/tools/Rscript --args $infile $outfile The input is never a big problem in galaxy, but how to capture the output was not so clear to me. So, Ma ...
written 7.2 years ago by Bree, Freddy de80
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Sorter Function Failure
... Dear Galaxy team, the sorter function under filters has a defect: it only ever sorts on the c1 column always in ascending order, alphabetical style We tried many times with a test data file. However, it DOES work on the main.g2.bx.psu.edu site. So, the local galaxy-dist is the problem. Could y ...
galaxy written 7.2 years ago by Bree, Freddy de80
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Answer: A: Running R In Galaxy
... Thanks again! This solves it I think. I re-directed this to galaxy-user, because it is clear that some of you do not know this either. ;) ________________________________________ To: Bree, Freddy de Subject: Re: [galaxy-user] running R in Galaxy Yes, tools/stats/r_wrapper.sh ...
written 7.2 years ago by Bree, Freddy de80
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Answer: A: Running R In Galaxy
... Dear all, In addition tot he previous. I can feed the source file (Rfile) and the data file to the system() call for R, but how do I capture the output back in perl? Freddy ...
written 7.2 years ago by Bree, Freddy de80
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Running R In Galaxy
... I've been trying to run R in Galaxy. 1. Running it as "R" is a hassle, because Galaxy cannot deal with source and input file and output file using "--args" and "<" (< in xml) and ">" (> in xml). 2. Running it through "perl" is also a hassle, because Galaxy needs to have an inpu ...
galaxy written 7.2 years ago by Bree, Freddy de80

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