[galaxy-user] Rscript not found when running shell script in Galaxy

Dear users, Has anyone encountered this problem before? I wrote a shell script which among other things calls some R scripts like this.. Rscript rscript_to_use.R When I run it via terminal it's fine plus I have verified Rscript works. But when I upload my tool to Galaxy and try to run it I

[galaxy-user] Galaxy Join takes too long?

I'm trying to joint two large intervals (one with 800,000 intervals and the other with about 350,000 intervals) using operates on intervals  join tool . I have no idea how long it should takes normaly. Two days have past and it is still runnig. Is there any limitation in file size for this

[galaxy-user] cufflinks output for cummeRbund

I have been using cufflinks on Galaxy Main.  I have downloaded the files generated but they do not correspond to the file names expected by cummeRbund.   For example: cummeRbund expects 4 tracking files (e.g isoforms.fpkm_tracking) , 4 .diff files (e.g isoform_exp.diff).   Here is a trimmed

Re: [galaxy-user] Galaxy Join takes too long?

Hello Milad, I am not sure if you are using the public Galaxy Main server (https://main.g2.bx.psu.edu) or your own local computer, or if the jobs are yellow and running or still grey and in the waiting-to-run stage. If using Galaxy Main, and if actually running (dataset is yellow), this

Re: [galaxy-user] Galaxy Join takes too long?

Hi Jen Thanks for your information, I'm using the public Galaxy main server and the job is yellow.It was a good point, I put the large dataset as the second input, I will wait  if no success I will treat as you said. Milad Bastami PhD student of Medical Genetics Department of Medical Genetics

Re: [galaxy-user] cufflinks output for cummeRbund

Cummerbund is available in the Galaxy toolshed for use in local or cloud Galaxies: http://toolshed.g2.bx.psu.edu/view/jjohnson/cummerbund We haven't put it on our public server yet because there are testing and compatibility challenges that need to be addressed. Best, J. On Feb 11, 2013, at

[galaxy-user] hg19 reference gnome for Tophat2

I downloaded the entire directory of UCSC for the reference gnome of Tophat2. It turns out that the Tophat2 and Bowtie2 uses the same reference gnome. I found a directory: Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index with the files: genome.1.bt2 genome.2.bt2 genome.3.bt2 genome.4.bt2

Re: [galaxy-user] hg19 reference gnome for Tophat2

Also, do I have make all the reference files executable? On Wed, Feb 13, 2013 at 6:39 AM, Sachit Adhikari sachit.techner...@gmail.com wrote: I downloaded the entire directory of UCSC for the reference gnome of Tophat2. It turns out that the Tophat2 and Bowtie2 uses the same reference gnome.