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primer3-org / primer3

Primer3 is a command line tool to select primers for polymerase chain reaction (PCR).
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unable to open file /opt/primer3_config/stack.ds #61

Closed Hytham79 closed 2 years ago

Hytham79 commented 2 years ago

I am trying to use a script to call primers posted on eulaf/cardio_padlock github page . I had primer3_core issue as not found in the beginning and I ended up setting the path correctly. Now when I run the script again, I get the error above. The P3CONFIG PATH is written as follow "/opt/primer3_config/". I am looking for some help to find a solution to pass that error. Note* I am using the virtual box with ensembl105 included. Thank you

untergasser commented 2 years ago

You are missing the primer3_config folder which comes with Primer3. I think this is more a question for eulaf/cardio_padlock to fix their script.

Best, Andreas

Hytham79 commented 2 years ago

I do have the primer3_config folder included in the primer3-2.4.0 version I downloaded. It has group of files where stack.ds file among them.

untergasser commented 2 years ago

So we did all we could with Primer3. I still would recommend to get the latest version of Primer3. The rest is in the responsibility of eulaf/cardio_padlock which sets most likely the path somewhere. Good luck!

Best, Andreas

Hytham79 commented 2 years ago

Thanks for your feed back.

Hytham79 commented 2 years ago

I see three assets"primer3-2.6.1_exe_for_windows.zip, source code(zip), and source code(tar.gz)" under the new version. which one I should download and works for Linux? I am using the virtual box. Thanks for your time

untergasser commented 2 years ago

Why not build from source? Follow the steps to install: https://github.com/primer3-org/primer3

If you have the latest version, search for the parameter PRIMER_THERMODYNAMIC_PARAMETERS_PATH in your script and delete the line. Primer3 will use the internal version.

Hytham79 commented 2 years ago

Thank you for your help. That solved the issue