Mercurial > repos > fubar > brokenandnotdeletablebyowneroradmin
changeset 16:36df24947ab3
readme changes
| author | Ross Lazarus <ross.lazarus@gmail.com> |
|---|---|
| date | Mon, 04 Jun 2012 16:22:51 +1000 |
| parents | 8594478e8d2c |
| children | 187c8b023595 |
| files | README.txt |
| diffstat | 1 files changed, 13 insertions(+), 8 deletions(-) [+] |
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--- a/README.txt Mon Jun 04 11:06:41 2012 +1000 +++ b/README.txt Mon Jun 04 16:22:51 2012 +1000 @@ -35,23 +35,28 @@ **Tool Generation option** Once the script is working with test data, this tool will optionally generate a new Galaxy tool in a gzip file ready to upload to your local toolshed for sharing and installation. -**Permission to to use this tool** must be explicitly granted by an administrator adding approved Galaxy user IDs to the local tool XML list of permitted users. *It will not run otherwise* +**Permission to to use this tool** must be explicitly granted by an administrator adding approved Galaxy user IDs to the local tool XML list +of permitted users. *It will not run otherwise* -**Note to system administrators** This tool offers *NO* built in protection against malicious scripts and should only be installed on private/personnal Galaxy instances. -Under no circumstances should you allow any user to use this tool unless you really, really trust them with the power to do what they want as the Galaxy user. +**Note to system administrators** This tool offers *NO* built in protection against malicious scripts and should only be installed on private/personal +Galaxy instances. Under no circumstances should you allow any user to use this tool unless you trust them with the power to do what they want +as the Galaxy user. -The tools generated by this tool will run just as securely as any other normal installed Galaxy tool but like any other new tools, should always be checked carefully before installation. +The tools generated by this tool will run just as securely as any other normal installed Galaxy tool but like any other new tools, should always +be checked carefully before installation. **Use on public servers** is STRONGLY discouraged for obvious reasons -**Scripting conventions** The pasted script will be executed with the path to the (optional) input tabular data file path or NONE if you do not select one, and the path to the optional -output file or None if none is wanted, as the first and second command line parameters. The script must deal appropriately with these - see Rscript examples below. -Note that if an optional HTML output is selected, all the output files created by the script will be nicely presented as links, with pdf images linked as thumbnails in that output. +**Scripting conventions** The pasted script will be executed with the path to the (optional) input tabular data file path or NONE if you do not +select one, and the path to the optional output file or None if none is wanted, as the first and second command line parameters. The script must +deal appropriately with these - see Rscript examples below. Note that if an optional HTML output is selected, all the output files created by +the script will be nicely presented as links, with pdf images linked as thumbnails in that output. This can be handy for complex scripts creating lots of output. **Simple examples** -A simple Rscript "filter" showing how the command line parameters can be handled, takes an input file, does something (transpose in this case) and writes the results to a new tabular file:: +A simple Rscript "filter" showing how the command line parameters can be handled, takes an input file, +does something (transpose in this case) and writes the results to a new tabular file:: # transpose a tabular input file and write as a tabular output file ourargs = commandArgs(TRUE)