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yyoshiaki / VIRTUS

A bioinformatics pipeline for viral transcriptome detection and quantification considering splicing.
https://github.com/yyoshiaki/VIRTUS/wiki
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singularity mode #40

Open antoine4ucsd opened 1 month ago

antoine4ucsd commented 1 month ago

Hello thank you for developing VIRTUS and VIRTUS2. great tools I would need to use them in singulality mode trying to run the following

cwltool --rm-tmpdir --singularity  ./VIRTUS.PE.singlevirus.cwl VIRTUS.PE.singlevirus.SRR26589924_1.moderna.sg.yaml

but I keep getting this error

^[[1;30mINFO^[[0m /mypath/miniconda3/envs/virtus_env/bin/cwltool 3.1.20220913185150
^[[1;30mINFO^[[0m Resolved './VIRTUS.PE.singlevirus.cwl' to 'file:///mypath/_virtus/VIRTUS/workflow/VIRTUS.PE.singlevirus.cwl'
^[[1;30mERROR^[[0m ^[[31mI'm sorry, I couldn't load this CWL file, try again with --debug for more information.
The error was: NodeJSEngine requires Node.js engine to evaluate and validate Javascript expressions, but couldn't find it.  Tried nodejs, node, singularity run node:alpine^[[0m

same error when trying to run virtus2 I am probably missing something obvious here... thank you!