Does Galaxy have a tool to run R script?
Dear all, I want to build a Galaxy tool to run R script. Do you know if there is already such tool or similar function? If you can share with me, I would very appreciate your help. Thank you, Bo Liu
Dear all,
I want to build a Galaxy tool to run R script. Do you know if there is already such tool or similar function? If you can share with me, I would very appreciate your help.
Hi Bo Liu, In my Galaxy instance I added few tools running with R. Here I just wrote a bash wrapper script to run the R program. Something like this: a) tool.xml file <command> /home/foo/tools/deseq/src/deseq.sh $anno_input.select_anno_format $anno_out $deseq_out $bam_alignments1 $bam_alignments2 >> $Log_File </command> b) deseq.sh file ## calling R script cat ../src/difftest_deseq.R | /usr/bin/R --slave --args $tmpfile ${DESEQ_RES} Hope this will solve your issue ! --Vipin
Thank you, Bo Liu ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Thank you, Vipin. Your information is very helpful. Regards, Bo On Sat, Jul 30, 2011 at 2:13 PM, Vipin TS <vipin.ts@gmail.com> wrote:
Dear all,
I want to build a Galaxy tool to run R script. Do you know if there is already such tool or similar function? If you can share with me, I would very appreciate your help.
Hi Bo Liu, In my Galaxy instance I added few tools running with R. Here I just wrote a bash wrapper script to run the R program. Something like this: a) tool.xml file <command> /home/foo/tools/deseq/src/deseq.sh $anno_input.select_anno_format $anno_out $deseq_out $bam_alignments1 $bam_alignments2 >> $Log_File </command> b) deseq.sh file ## calling R script cat ../src/difftest_deseq.R | /usr/bin/R --slave --args $tmpfile ${DESEQ_RES} Hope this will solve your issue ! --Vipin
Thank you, Bo Liu ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
You can also directly link the R script in the galaxy-tool. We have many of those. For testing (NOT SAFE!) we also have a tool that allows the upload of an R script for testing purposes.... See the arhives for more extensive discussion... <command> R --slave --vanilla --file=$GALAXY_ROOT_DIR/tools/somedir/somescript.R --args $input1 $options $output1 </command> http://gmod.827538.n3.nabble.com/Re-galaxy-user-plugging-R-into-galaxy-td187... Good luck! Alex ________________________________________ Van: galaxy-dev-bounces@lists.bx.psu.edu [galaxy-dev-bounces@lists.bx.psu.edu] namens liu bo [liubo03@gmail.com] Verzonden: zaterdag 30 juli 2011 6:49 Aan: galaxy-dev@lists.bx.psu.edu Onderwerp: [galaxy-dev] Does Galaxy have a tool to run R script? Dear all, I want to build a Galaxy tool to run R script. Do you know if there is already such tool or similar function? If you can share with me, I would very appreciate your help. Thank you, Bo Liu ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Dear Alex, Thanks a lot for your useful information. --Bo On Mon, Aug 1, 2011 at 5:18 AM, Bossers, Alex <Alex.Bossers@wur.nl> wrote:
You can also directly link the R script in the galaxy-tool. We have many of those. For testing (NOT SAFE!) we also have a tool that allows the upload of an R script for testing purposes.... See the arhives for more extensive discussion... <command> R --slave --vanilla --file=$GALAXY_ROOT_DIR/tools/somedir/somescript.R --args $input1 $options $output1 </command>
http://gmod.827538.n3.nabble.com/Re-galaxy-user-plugging-R-into-galaxy-td187...
Good luck!
Alex
________________________________________ Van: galaxy-dev-bounces@lists.bx.psu.edu [galaxy-dev-bounces@lists.bx.psu.edu] namens liu bo [liubo03@gmail.com] Verzonden: zaterdag 30 juli 2011 6:49 Aan: galaxy-dev@lists.bx.psu.edu Onderwerp: [galaxy-dev] Does Galaxy have a tool to run R script?
Dear all,
I want to build a Galaxy tool to run R script. Do you know if there is already such tool or similar function? If you can share with me, I would very appreciate your help.
Thank you, Bo Liu ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
participants (3)
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Bossers, Alex -
liu bo -
Vipin TS