cummerbund and cuffdiff error on local galaxy

Question: cummerbund and cuffdiff error on local galaxy

3.4 years ago by

biowz • 0

United States

biowz • 0 wrote:

This is my first to run this software on local galaxy. I met this problem. Would like to help me solve this problem? Thank you very much!

Fatal error: Exit code 1 (CummerBund Error) Error running R script. /bin/sh: Rscript: command not found

For cuffdiff and cuffdiff for cummerbund tools, I met the following information, is it right?

Log: tool progress Log: tool progress [16:42:58] Loading reference annotation. Warning: No conditions are replicated, switching to 'blind' dispersion method [16:42:59] Inspecting maps and determining fragment length distributions. [16:43:00] Modeling fra

software error • 1.2k views

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modified 3.4 years ago • written 3.4 years ago by biowz • 0

3.4 years ago by

Bjoern Gruening ♦ 5.1k

Germany

Bjoern Gruening ♦ 5.1k wrote:

This indicates that you don't have R installed or on your $PATH, which is strange because R should be a dependency of cummerbund.

Can you check if R is installed?

ADD COMMENT • link written 3.4 years ago by Bjoern Gruening ♦ 5.1k

I checked the status of R under admin/manage installed tools, I found that the status of package_perl_5_18 and package_r_3_1_2 is "installed,missing repository dependencies" How to repair these bugs?

ADD REPLY • link written 3.4 years ago by biowz • 0

3.4 years ago by

biowz • 0

United States

biowz • 0 wrote:

Thank you very much for your reply. Do you think cuffdiff is right or not. By the way, I am not sure whether R is one of cummerbund. The read file as follow:

CummeRbund is an R package that is designed to aid and simplify the task of analyzing Cufflinks RNA-Seq output.
( http://compbio.mit.edu/cummeRbund/ )

Prerequisites for installing cumme=Rbund:
The linux package: libxml2-dev
In ubuntu:   sudo apt-get install libxml2-dev

R package: ggplot2
   install.packages("ggplot2",dependencies = TRUE)

To install cummeRbund on your R server, follow the directions in:
( http://www.bioconductor.org/packages/release/bioc/html/cummeRbund.html )
   source("http://bioconductor.org/biocLite.R")
   biocLite("cummeRbund")

This galaxy tool package includes a replacement variation of the cuffdiff wrapper that will generate an output that can be used directly in cummeRbund.

I never install R in my computer independently. If I install R, how to make a path to let cummerbund in galaxy recognize? Thank you very much!

ADD COMMENT • link written 3.4 years ago by biowz • 0

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