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
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.