Question: Deseq2 error running R script
1
gravatar for amitpande74
13 months ago by
amitpande7410
amitpande7410 wrote:

Hi, I am having problems in running deseq2 package in my local galaxy installation. It says R broken pipe and stops. Kindly help.

![Deseq2 error] galaxy_deseq2_error
the host gif

rna-seq • 486 views
ADD COMMENTlink modified 13 months ago • written 13 months ago by amitpande7410
0
gravatar for Jennifer Hillman Jackson
13 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello Amit,

Please update the tool to the latest version DESeq2 (version 2.11.39) from the tool shed. Also, be sure that Galaxy itself is updated to 17.01 and that the default Conda dependency resolution function is left intact and used for the tool install.

Let us know if that does not work. The correction is new and still undergoing an update at Galaxy Main (http://usegalaxy.org) plus testing in a default local.

Hope you are doing well! Jen, Galaxy team

ADD COMMENTlink written 13 months ago by Jennifer Hillman Jackson25k
0
gravatar for amitpande74
13 months ago by
amitpande7410
amitpande7410 wrote:

Hi Jennifer,

I thought I had cracked the problem by configuring R. But the package I was trying to install is deseq2_hts from the tool shed repository. The deseq_config.sh.sample for this package requires oqtans package. Since this package depends on octave etc from the oqtans ....it seems like a never ending quest. I think if this is also provided with the dependencies it might ease the task for people like me. I shall revert to you if it does not work.

thanks, Amit.

ADD COMMENTlink written 13 months ago by amitpande7410
0
gravatar for amitpande74
13 months ago by
amitpande7410
amitpande7410 wrote:

Hi Jennifer,

I tried all possible ways to install deseq2_hts ...updated the galaxy version to 17.01...but still it requires oqtans to be installed which is not available in the dependencies. The fact with deseq2_hts is that one can analyze BAM files and then take the count tables to analyze them further..then I wrote to one of the authors of oqtans ...giving him the details and asking for help. With his advice, I downloaded oqtans from github , but the problem is that the config file of oqtans does not take the root path ....I have installed it in the config folder in galaxy.

Kindly advise.

ADD COMMENTlink written 13 months ago by amitpande7410
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