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blahah / transrate

Understand your transcriptome assembly
http://hibberdlab.com/transrate
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Salmon #223

Open weedcentipede opened 6 years ago

weedcentipede commented 6 years ago

Hello, Trying to run Transrate, I get the following error for Salmon, 

bio@biocomp06:~/Documents/Purpureocillium/Transcriptomica/Transrate$ transrate --assembly=assembly31.scafSeq,assembly55.scafSeq,assembly73.scafSeq,assembly99.scafSeq,transcripts_k33.fasta,transcripts_k55.fasta,transcripts_k73.fasta,transcripts_k99.fasta,Trinity.fasta --right=output_forward_paired.fq --left=output_reverse_paired.fq --threads=4 --output=SOAPvsTrinityvsSPADES 
[DEPRECATION] This gem has been renamed to optimist and will no longer be supported. Please switch to optimist as soon as possible.
Dependencies are missing:
  - salmon (0.4)
To install all missing dependencies, run:
  transrate --install-deps all
If you only want the read-metrics dependencies:
  transrate --install-deps read
Or if you only want the reference-metrics dependencies: 
  transrate --install-deps ref
bio@biocomp06:~/Documents/Purpureocillium/Transcriptomica/Transrate$ transrate --install-deps all
[DEPRECATION] This gem has been renamed to optimist and will no longer be supported. Please switch to optimist as soon as possible.
Checking dependencies
Installing salmon (0.4)...
[ERROR] 2018-10-06 17:38:02 : Failed to install: 
 - salmon:0.4

Trying to fix this, I installed with Conda and still getting the same error, 

bio@biocomp06:~/Documents/Purpureocillium/Transcriptomica/Transrate$ salmon -v
salmon 0.11.2
bio@biocomp06:~/Documents/Purpureocillium/Transcriptomica/Transrate$ which salmon
/home/bio/anaconda3/bin/salmon

Do you know how can I fix this? Thanks in advance, Luis Alfonso.

podunn58 commented 5 years ago

I am having this same problem. It will not install Salmon 0.4 with the --install-deps all command, and Salmon 0.4 is so old that it is not on conda anymore.
Any assistance would be appreciated. thanks, Peter