3

I'm getting this error on my mac osx build.

Primer3/eprimer3 issue:

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. In Linux, there are two default locations that are tested if this tag is not defined: ./primer3_config/ and /opt/primer3_config/. For Windows, there is only one default location: .\primer3_config\.

I put the primer3_config in my PATH in bin and still cannot solve this issue. 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.

datz
  • 51
  • 1
  • 4

2 Answers2

3

According to the primer3 manual:

1.5. IMPORTANT: because PRIMER_THERMODYNAMIC_ALIGNMENT=1

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

So if you download and compile primer3 form source using the Make command, to get primer3 to run globally you need to copy the executueable, primer3_core, to your path and place the configuration directory, primer3_config in that same directory or at /opt/primer3_config

cd src
sudo cp primer3_core /usr/local/bin # or /usr/bin
sudo cp -r primer3_config /opt/
zach
  • 29,475
  • 16
  • 67
  • 88
1

I has the same issue. I had installed Primer 3 using homebrew-science which was pretty painless. https://github.com/Homebrew/homebrew-science

I did try copying the primer3_config directory into the homebrew primer3 directory, ie:

/usr/local/Cellar/primer3/2.3.4/bin/primer3_config but this also did not work.

In the end I added the PRIMER_THERMODYNAMIC_PARAMETERS_PATH configuration to the primer 3 input file, and this worked. Note that the directory name must have a trailing slash. It 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
port5432
  • 5,889
  • 10
  • 60
  • 97