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EI-CoreBioinformatics / mikado

Mikado is a lightweight Python3 pipeline whose purpose is to facilitate the identification of expressed loci from RNA-Seq data * and to select the best models in each locus.
https://mikado.readthedocs.io/en/stable/
GNU Lesser General Public License v3.0
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Transdecoder error with -G Universal parameter #312

Closed LehmannN closed 4 years ago

LehmannN commented 4 years ago

Hello !

I have another comment regarding the daijin pipeline. When coming through the TransDecoder.LongOrfs step in the daijin mikado pipeline, it suddenly stops with the error "Sorry, Universal is not currently supported or recognized.". So I just ran transdecoder out of the daijin pipeline without the -G Universal parameter, but I wonder it there is a way to modify the command line ran by daijin ? I am using the Mikado conda environment btw and we get the same error for TransDecoder.Predict.

Thanks again help and comments.

lucventurini commented 4 years ago

Dear @LehmannN ,

This is really surprising, I automatically check that Daijin runs correctly whenever there is a commit. May I ask which version of TransDecoder you are using? On my workstation Universal is explicitly listed as a valid option (with conda, transdecoder=5.5.0=pl526_2).

LehmannN commented 4 years ago

I found that I am running TransDecoder-3.0.1 so that might explain why. I have it installed locally and through the conda environment but the default program that runs is the one installed locally... I am not sure how to fix that but will have a look.

LehmannN commented 4 years ago

I realized that in fact I had no installation of transdecoder in conda, only a local installation. I have been fooled by running mikado inside the conda environment, but since the tool was not in the environment, daijin found it in /usr/bin/. Is there a reason why you don't have transdecoder and mikado in the environment.yml file ?

lucventurini commented 4 years ago

Dear @LehmannN ,

Within Daijin, I try to keep the different tool requirements separate, also because there are tools that are incompatible with each other (e.g. I think that tophat2 requires python2, which would make it incompatible with Mikado itself). For this reason, Daijin fully implements the --use-conda switch present also in Snakemake. Briefly, if the switch is present on the command line, Daijin will create a separate Conda environment for each required tool, including TransDecoder.

I hope this helps.

Kind regards

LehmannN commented 4 years ago

Ok, thanks for the explanations !