Re: [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.
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
${DESEQ_RES}
Hope this will solve your issue !
--Vipin
Thank you,
Bo Liu
___
Please keep all replies on the list by using reply all
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
___
Please keep all replies on the list by using reply all
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
[galaxy-dev] job status when SGE kills/aborts job
On Saturday, July 30, 2011, Shantanu Pavgi pa...@uab.edu wrote: The -V option is not for verbose mode but for exporting your shell environment. Refer to qsub manual for details: Specifies that all environment variables active within the qsub utility be exported to the context of the job. We are already using it in our configuration as needed. That is such a common need it would be great to have it in the Galaxy documentation as an example of using native SGE options with drmaa:// in universe_wsgi.ini Plus the http://linux.die.net/man/5/sge_complex link. Thanks! I think we are having problem with the galaxy (or drmaa Python lib) parsing correct drmaa/SGE messages and not with the drmaa URL configuration. Thoughts? I'd try adding a few debug log/print statements to the code to try and diagnose it. Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] exporting environment variables to SGE in galaxy
Hi Shantanu,
Thanks for the information! This did the trick.
Chaolin
On Jul 30, 2011, at 1:28 AM, Shantanu Pavgi wrote:
On Jul 29, 2011, at 11:28 PM, Chaolin Zhang wrote:
Hi,
I am setting up SGE in our galaxy mirror. One problem I have is that I
cannot export environment variables of the specific users running the galaxy
service. On command line, I did this by qsub -V script.sh. or add a line
#$ -V
in script.sh
I tried to change
/lib/galaxy/jobs/runners/sge.py and lib/galaxy/jobs/runners/drmaae.py
by adding a line
#$ -V
under
sge_template = #!/bin/sh
#$ -S /bin/sh
but this did not help.
Any idea is very appreciated!
Chaolin
Chaolin,
I don't think you will need to modify source code for this. Adding -V
option to the drmaa URL should be sufficient. For example:
{{{
drmaa:// -V /
}}}
Hope this helps.
--
Shantanu.
___
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/
[galaxy-dev] move dataset from history to server
Hello, Is there a way to copy/move a dataset located in the history to a given location in the filesystem? As an administrator you can upload data from given directory to your datalibrary. Is there a way to do the opposite? I know that it is possible to download any dataset to your local computer but what I want is just to move the dataset constructed by galaxy to a given repository in my server filesystem. thank you, colin ___ 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/
Re: [galaxy-dev] job status when SGE kills/aborts job
On Jul 30, 2011, at 4:58 AM, Peter Cock wrote: On Saturday, July 30, 2011, Shantanu Pavgi pa...@uab.edu wrote: The -V option is not for verbose mode but for exporting your shell environment. Refer to qsub manual for details: Specifies that all environment variables active within the qsub utility be exported to the context of the job. We are already using it in our configuration as needed. That is such a common need it would be great to have it in the Galaxy documentation as an example of using native SGE options with drmaa:// in universe_wsgi.ini Plus the http://linux.die.net/man/5/sge_complex link. Thanks! I think we are having problem with the galaxy (or drmaa Python lib) parsing correct drmaa/SGE messages and not with the drmaa URL configuration. Thoughts? I'd try adding a few debug log/print statements to the code to try and diagnose it. Peter The option is the same for Torque/PBS as well. We'll have the chance (or misfortune depending on how you look at it) of testing both SGE and Torque locally. chris ___ 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/
