Question: Difficulties in Trinity installation
0
gravatar for adnan.lahuf
4 weeks ago by
adnan.lahuf0 wrote:

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

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ADD COMMENTlink modified 4 weeks ago • written 4 weeks ago by adnan.lahuf0
2
gravatar for Philipp Bayer
4 weeks ago by
Philipp Bayer6.6k
Australia/Perth/UWA
Philipp Bayer6.6k wrote:

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.

ADD COMMENTlink written 4 weeks ago by Philipp Bayer6.6k
0
gravatar for adnan.lahuf
4 weeks ago by
adnan.lahuf0 wrote:

Thank Philip for attention and reply. Regards

ADD COMMENTlink written 4 weeks ago by adnan.lahuf0

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:

  1. Copy the contents of your reply from this answer (you can edit this answer (Ctrl/Cmd + click the link to open it in a new tab) and do a Select All -> Copy there).
  2. Click on Add Comment on Phillipp's post here: A: Difficulties in Trinity installation
  3. Paste the copied text
  4. Click on the green Add Comment button
  5. Click on moderate back in your answer here: A: Difficulties in Trinity installation
  6. Choose Delete Post
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Thank you!

P.S: Please do not add answers unless you're answering the top level question. Use Add Comment or Add Reply as appropriate.

ADD REPLYlink written 4 weeks ago by RamRS25k
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