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matdoering / openPrimeR

An R Package for Multiplex PCR Primer Design and Analysis
http://openprimer.mpi-inf.mpg.de
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Please define the UNAFOLDDAT variable in your path before using OligoArrayAux. #2

Closed jxshi closed 4 years ago

jxshi commented 4 years ago

Hi,

I tried to use openPrimeR package on my machine. I have already set UNAFOLDDAT path in ~/.bashrc file by adding this line export UNAFOLDDAT=/home/jshi/biosoft/oligoarrayaux-3.8/data, but error message popped up as listed follow. 

> settings <- read_settings(settings.xml)
Reading settings file: C_Taq_PCR_high_stringency.xml
Due to missing external tools the following constraints were ignored:cross_dimerization,self_dimerization
Due to missing external tools the following coverage constraints were ignored:coverage_model
Warning message:
In check.tool.function() :
  Please define the UNAFOLDDAT variable in your path before using OligoArrayAux.

I typed echo $UNAFOLDDAT command and it returned:

/home/jshi/biosoft/oligoarrayaux-3.8/data

Can you check for me please?

Thank you and best wishes!

Jianxiang

jxshi commented 4 years ago

I solved the problem by add :$PATH to the end of the last line. export UNAFOLDDAT=/home/jshi/biosoft/oligoarrayaux-3.8/data:$PATH worked. Will check out how the package works tomorrow. Thank you and cheers!

Jianxiang

warthmann commented 4 years ago

Not sure why and how the above works. I suggest to set the variables for openPrimeR (the PATH variable as well as UNAFOLDDAT) in the respective R-script like so :

old_path <- Sys.getenv("PATH") new_path <- old_path new_path <- paste(new_path, "/Library/TeX/texbin", sep = ":") new_path <- paste(new_path, "/Users/xy/miniconda3/envs/openprimer/bin/", sep = ":") new_path <- paste(new_path, "/Users/xy/Applications/MELTING5.2.0/executable", sep = ":") Sys.setenv(PATH = new_path) Sys.setenv(UNAFOLDDAT = "/Users/xy/miniconda3/envs/openprimer/share/oligoarrayaux")

In addition I set them in the ˜/.profile, but that didn't seem to do it.