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  • chc*
    Junior Member
    • Jan 2016
    • 6

    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??
  • GenoMax
    Senior Member
    • Feb 2008
    • 7142

    #2
    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.

    Comment

    • Blahah404
      Member
      • Dec 2011
      • 48

      #3
      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.

      Comment

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