problem with Trinity command run in denovo transcriptome assembly
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10 months ago
Aliviya • 0

I tried to run my Trinity command for the assembly but this is the error I've been getting .. please help let me know where did I go wrong. I'm new to this analysis field.

Error, cannot locate Trinity-specific tool: ParaFly in the PATH setting: /usr/local/bin/trinity-plugins/BIN:/home/aliviya21/anaconda3/bin:/home/aliviya21/anaconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/aliviya21/Downloads/bowtie2-2.4.1:/home/aliviya21/BIONIVID/trinityrnaseq-v2.13.0,  be sure to install Trinity by running 'make' in the base installation directory


analysis trinity transcriptome denovo • 498 views
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Use conda to install. conda create -n trinity trinity and then conda activate trinity should do it. Reference: Creating workflows with snakemake and conda

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I did the same prior, created an env and tried running the program. This is the error I've been getting the same one with or without an environment. . Error, cannot locate Trinity-specific tool: ParaFly in the PATH setting: /usr/local/bin/trinity-plugins/BIN:/home/aliviya21/anaconda3/envs/trinity/bin:/home/aliviya21/anaconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/aliviya21/Downloads/bowtie2-2.4.1:/home/aliviya21/BIONIVID/trinityrnaseq-v2.13.0, be sure to install Trinity by running 'make' in the base installation directory