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Old 03-31-2016, 04:34 AM   #1
chc*
Junior Member
 
Location: Devon, UK

Join Date: Jan 2016
Posts: 6
Default Transrate for metatranscriptome data

Hi all,

I am trying to install and use Transrate to assess the quality of different assemblies of some metatranscriptome data I have. However when I use gem install and then try to install dependencies this is what I get:
$ sudo /users/bmg/chc/bin/transrate --install-deps read
[sudo] password for chc:
Checking dependencies
Installing snap (1.0beta.18)...
Installing bam-read (1.0.0)...
Installing salmon (0.4)...
[ERROR] 2016-03-31 12:31:38 : Failed to install:
- salmon:0.4

Does anyone have any ideas how to work around this non- informative error??
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Old 03-31-2016, 05:13 AM   #2
GenoMax
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Location: East Coast USA

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Posts: 7,077
Default

Not a direct answer for your question.

If you are referring to salmon (counting program) then 0.4 is an old version. Perhaps you could manually install salmon binaries from here: https://github.com/COMBINE-lab/salmon/releases If transrate requires that particular version then you could try installing that manually.
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Old 03-31-2016, 07:16 AM   #3
Blahah404
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Location: Cambridge, UK

Join Date: Dec 2011
Posts: 48
Default

Hi chc, transrate author here.

For some reason, transrate has tried to install the salmon dependency but can't find it afterwards. It might be related to using sudo - you shouldn't have to use sudo with transrate and doing so is likely to cause problems (because sudo often leads to a different user space being visible to the programs it runs).

The easiest way to install transrate, and the recommended option unless you want to use it as a dependency in a Ruby program, is to use the pre-packaged install.

You can grab 1.0.1 here: https://github.com/Blahah/transrate/releases/tag/v1.0.1

I'll be releasing a new version ASAP, hopefully today, with the latest Salmon release, but 1.0.1 should work fine.
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