Why am I getting this error on my Mac OSX Primer3 / eprimer3 build?

I am getting this error on my mac osx build.

The problem with Primer3 / eprimer3:

Error: thermodynamic approach chosen, but path to thermodynamic parameters not specified

      

From:

http://www.mcardle.wisc.edu/mprime/help/primer3/primer3_manual.htm#globalTags

PRIMER_THERMODYNAMIC_PARAMETERS_PATH (string; default ./primer3_config)

      

This tag specifies the path to the directory that contains all the parameter files used by the thermodynamic approach. On Linux, there are two default locations that are checked if this tag is not defined: ./primer3_config/

and /opt/primer3_config/

. For Windows, there is only one default location: .\primer3_config\

.

I put primer3_config in my PATH in bin and still cannot solve this problem. I even did:

export PRIMER_THERMODYNAMIC_PARAMETERS_PATH=/Users/jared/Downloads/primer3-2.3.2/src

      

and

export PRIMER_THERMODYNAMIC_PARAMETERS_PATH=/Users/jared/Downloads/primer3-2.3.2/src/primer3_config

      

to no avail.

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2 answers


According to primer3 manual:

1.5. IMPORTANT: because PRIMER_THERMODYNAMIC_ALIGNMENT=1 

      

PRIMER_THERMODYNAMIC_PARAMETERS_PATH should point to the correct location. This tag specifies the path to the directory that contains all the parameter files used by the thermodynamic approach. Linux has two default locations that are tested if this tag is not define: ./ primer3_config / and / opt / primer3_config /. For Windows, there is only one default location:. \ Primer3_config. If the parameter files are not in the same location, be sure to set PRIMER_THERMODYNAMIC_PARAMETERS_PATH.



So, if you download and compile primer3 source using the command Make

to run primer3 globally, you need to copy the executable primer3_core

to your path and place the config directory primer3_config

in that same directory or in/opt/primer3_config

cd src
sudo cp primer3_core /usr/local/bin # or /usr/bin
sudo cp -r primer3_config /opt/

      

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I have the same problem. I installed Primer 3 using homebrew-science , which was pretty painless. https://github.com/Homebrew/homebrew-science

I tried to copy the primer3_config directory to the primer3 homebrew directory, that is:

/usr/local/Cellar/primer3/2.3.4/bin/primer3_config, but that didn't work either.

In the end, I added the PRIMER_THERMODYNAMIC_PARAMETERS_PATH config to the primer 3 input file and it worked. Note that the directory name must have a trailing slash. This is the last entry in the file below, which is copied from the example file in the primer3 sources.



SEQUENCE_ID=example
SEQUENCE_TEMPLATE=GTAGTCAGTAGACNATGACNACTGACGATGCAGACNACACACACACACACAGCACACAGGTATTAGTGGGCCATTCGATCCCGACCCAAATCGATAGCTACGATGACG
SEQUENCE_TARGET=37,21
PRIMER_TASK=pick_detection_primers
PRIMER_PICK_LEFT_PRIMER=1
PRIMER_PICK_INTERNAL_OLIGO=1
PRIMER_PICK_RIGHT_PRIMER=1
PRIMER_OPT_SIZE=18
PRIMER_MIN_SIZE=15
PRIMER_MAX_SIZE=21
PRIMER_MAX_NS_ACCEPTED=1
PRIMER_PRODUCT_SIZE_RANGE=75-100
P3_FILE_FLAG=1
SEQUENCE_INTERNAL_EXCLUDED_REGION=37,21
PRIMER_EXPLAIN_FLAG=1
PRIMER_THERMODYNAMIC_PARAMETERS_PATH=/usr/local/Cellar/primer3/2.3.4/bin/primer3_config/
=

      

Then run it like this:

$ primer3_core < example2

      

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