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Difficulties in Trinity installation

Hi Colleagues, I have tried to install the Trinity RNAseq. assembler in linux. However, I have faced a problem (Trinity Trinity-v2.9.0 requires salmon to be installed. Get it here: https://combine-lab.github.io/salmon/ at /home/adnan/Downloads/trinityrnaseq-v2.9.0/Trinity line 3936). Despit the fact that I have install the salmon and located it in usr/bin path.Could you please help me solving this problem. Regards Adnan Difficulties in Trinity installation

assembly
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written by adnan.lahuf • adnan.lahuf

1 answer

I think if you install Trinity via conda or if you use the Singularity or Docker images provided you can circumvent this problem.

What is the output of which salmon? That's what Trinity runs to check for your salmon installation. There's a chance that the salmon in /usr/bin/ isn't set to executable (chmod +x will solve that). If which salmon returns nothing then salmon isn't properly set up in /usr/bin.

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written by Philipp Bayer Philipp Bayer

Thank Philip for attention and reply. Regards

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written by adnan.lahuf • adnan.lahuf

Hi adnan.lahuf,

This reply should be a comment on Phillipp's answer. Could you make the appropriate change please? That would involve the following steps:

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written by Ram Ram

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