Question: DESeq2 Error on Cloudman
gravatar for madkisson
3.6 years ago by
United States
madkisson30 wrote:


I'm working on Cloudman doing RNASeq transcriptome analysis. I've made BAM file using TopHat2 and RefSeq mm10 gtf file for Junctions.

I'm now trying to Run these through DESeq2 for differential expression analysis, using the exact same gtf file. Right off the bat it fails, giving me this error:

/mnt/galaxy/shed_tools/ line 61: /samtools: No such file or directory

Any thoughts? I'm not sure which 'file' or 'directory' it's referring to

rnaseq galaxy cloudman deseq2 • 1.2k views
ADD COMMENTlink modified 3.6 years ago • written 3.6 years ago by madkisson30
gravatar for vipin
3.6 years ago by
United States
vipin20 wrote:

Might be a problem with your env variable PATH, which is not seeing the samtools version installed on the machine. You cah check for the samtools on your machine as 

which samtools 

and add that path to the 


Please let me know if that fix your problem.

ADD COMMENTlink written 3.6 years ago by vipin20

I'm using Cloudman. I think your answer is based on me using a local instance of Galaxy? I'm not sure I can do what you're suggesting from a browser version of Galaxy

ADD REPLYlink written 3.6 years ago by madkisson30

Due to this error, i did go in and install every SAMTools tool or package I could find into my tool shed. Nothing worked

ADD REPLYlink written 3.6 years ago by madkisson30
gravatar for Jennifer Hillman Jackson
3.6 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello - Are you using the "managed dependencies" option when installing tools? If not, try that. Also, on a cloud instance, you are the administrator. Instructions for how to ssh into the instance are in the admin panel. Once logged in, you can navigate through all of the configuration files and such just like any other unix system. This includes testing to see if the install path is known and adjusting the configuration files by doing what Vipin suggests. Thanks! Jen, Galaxy team

ADD COMMENTlink modified 3.6 years ago • written 3.6 years ago by Jennifer Hillman Jackson25k

Yes, manage dependencies is generally checked by default and I do not mess with it. I just tried un/reinstalling, along with a package_deseq2 and all tool dependencies. Just tried to run and got the same error.

ADD REPLYlink written 3.6 years ago by madkisson30

I don't know Unix so I'm not qualified to go in and start squirreling around with the entrails of this thing. Is that really going to be my only option here? 

ADD REPLYlink written 3.6 years ago by madkisson30

Hello, I believe that I figured out the issue.

The tool is being installed from the Main Tool Shed. It does not have managed dependencies from this source. The package for dependencies is a mismatch for this version of the tool (this is why it does not install automatically with the primary repository). I have noticed this before and was not exactly clear why it was present in the Main Tool Shed (perhaps was promoted early - or is used by another repository/tool). In general, one should never need to install a wrapper dependency "package" independently.

The tool exists in the Test Tool Shed as well. In this location, 2 out of 3 versions do have managed dependencies. However, since it has not been promoted to the Main Tool Shed yet, using any of the options could have issues. And while these could (and should) be reported to the tool author should you decide to use one of these wrapper versions (there are three), only testing/using will truly inform you of how robust any of these are (meaning: how much you can expect the install to go well - and trust that the results are accurate). Tools in the Test TS come in a range of "finished" states that can change quickly.

So there are two current choices:

1) Use the version from the Main TS, and try to find local admin help to aid in installing and configuring the dependencies. General instructions for tool installs are in the Galaxy wiki, under the Admin section, if you want to try. 

2) Use the version from the Test TS. There are three wrapper choices. The first two that will come up in the search (using keyword: deseq2) have managed dependencies, the third does not. How to detect this? Click into the tool and scroll down to examine the related repositories. If a dependency package is associated, then managed dependencies can be part of the install process. You can always contact the repository owner and ask about the status - such as when/if this will be promoted to the Main TS. And if not now, why - so that you can consider those reasons (risks associated with use, as determined by the author) before using. 

I realize that this is probably a frustrating answer. But such is the nature of tool/wrapper development. Not all tools are in a fully finished state and promoted to the Main TS. And new wrappers are created/modified daily on the Test TS. It takes active, ongoing work to author and maintain a tool wrapper. Galaxy updates and tool versions change. It up to the wrapper author to prioritize maintenance. All are open source and many tool wrappers were/are contributed by the community.

But, I hope this helps anyway - at least the error is clarified and the available choices for moving forward are clear now.

Best, Jen, Galaxy team

ADD REPLYlink modified 3.6 years ago • written 3.6 years ago by Jennifer Hillman Jackson25k

Thanks Jen 

I'll keep plugging away at the Test TS versions. I'll try and contact the admins and see what I can glean from them. Thanks. I kind of knew DESeq2 was going to be a problem because I'd gathered that it's fairly new in the Galaxy galaxy. If a fix presents itself I'll post back here.

ADD REPLYlink written 3.6 years ago by madkisson30
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