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我在我的 mac osx 构建中遇到了这个错误。

Primer3/eprimer3 问题：

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

从：

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

PRIMER_THERMODYNAMIC_PARAMETERS_PATH (string; default ./primer3_config)

此标记指定包含热力学方法使用的所有参数文件的目录的路径。在 Linux 中，如果未定义此标记，则会测试两个默认位置：./primer3_config/和/opt/primer3_config/. 对于 Windows，只有一个默认位置：.\primer3_config\.

我将primer3_config放在bin的PATH中，仍然无法解决这个问题。我什至做了：

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

和

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

无济于事。

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2 回答 2

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根据primer3手册：

1.5. IMPORTANT: because PRIMER_THERMODYNAMIC_ALIGNMENT=1

PRIMER_THERMODYNAMIC_PARAMETERS_PATH 必须指向正确的位置。此标记指定包含热力学方法使用的所有参数文件的目录的路径。在 Linux 中，如果未定义此标记，则会测试两个默认位置：./primer3_config/ 和 /opt/primer3_config/。对于 Windows，只有一个默认位置：.\primer3_config。如果参数文件不在这些位置之一，请务必设置 PRIMER_THERMODYNAMIC_PARAMETERS_PATH。

因此，如果您使用该Make命令下载并编译primer3表单源，要让primer3全局运行，您需要将可执行文件复制primer3_core到您的路径并将配置目录primer3_config 放在同一目录中或/opt/primer3_config

cd src
sudo cp primer3_core /usr/local/bin # or /usr/bin
sudo cp -r primer3_config /opt/
于 2013-02-06T19:05:18.593 回答
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
于 2013-06-15T08:35:36.963 回答