Re^4: Primer3 - BioPerl

For some reason it didn't really put my reply yesterday... But yeah, someone actually mentioned that yesterday! Never knew we had to download two separate packages. :: facepalm :: So, I have it running but receive an error (see the "UPDATE" in the main post).

The error I get as soon when dumping the results data structure via:

 my $results = $primer3->run;
print Dumper($results);
[download]

is "'PRIMER_ERROR' => 'thermodynamic approach chosen, but path to thermodynamic parameters not specified'". Not sure as to why this is, especially since it looks like that is not the default and I never passed anything in like that...hmm. Trying to modify it still, but got that error multiple times yesterday.

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Re^5: Primer3 - BioPerl by datz (Initiate) on Mar 26, 2012 at 02:50 UTC
I'm getting this same error on my mac osx build. Any luck solving this issue? `Primer3/eprimer3 issue: Error: thermodynamic approach chosen, but path to thermodynamic parame +ters not specified` [download] 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/pri +mer3-2.3.2/src` [download] and `export PRIMER_THERMODYNAMIC_PARAMETERS_PATH=/Users/jared/Downloads/pri +mer3-2.3.2/src/primer3_config` [download] to no avail.	[reply] [d/l] [select]
Re^6: Primer3 - BioPerl by Anonymous Monk on Apr 27, 2012 at 12:36 UTC
Try copying the src/primer3_config file from the primer3 build directory to /opt/primer3_config - it should look in there by default according to the docs (http://www.mcardle.wisc.edu/mprime/help/primer3/primer3_manual.htm)	[reply]
Re^7: Primer3 - BioPerl by tinu329 (Initiate) on Apr 01, 2013 at 16:08 UTC
I know its more than a year since the question is posted. Had to deal with the same problem and could solve using the below method. Thought of posting it, if it would be useful for anyone else. Thanks !! specify the PRIMER_THERMODYNAMIC_PARAMETERS_PATH in the input file for the primer3_core software cat inputfile.txt SEQUENCE_ID=example SEQUENCE_TEMPLATE=GTAGTCAGTAGACNATGACNACTGACGATGCAGACNACACACACACACACAG +CACACAGGTATTAGTGGGCCATTCGATCCCGACCCAAATCGATAGCTACGATGACG SEQUENCE_TARGET=37,21 PRIMER_TASK=generic 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=/home/User/Softwares/primer3-2.3. +5/src/primer3_config/ = [download] Thanks, Tinu	[reply] [d/l]