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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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Question:Due to missing external tools the following constraints were ignored:cross_dimerization,secondary_structure,self_dimerization #10

Closed YangLeng90 closed 2 years ago

YangLeng90 commented 2 years ago

According to https://www.bioconductor.org/packages/release/bioc/vignettes/openPrimeR/inst/doc/openPrimeR_vignette.html and try to reproduce the result inside.

when run :

settings.xml <- system.file("extdata", "settings", "C_Taq_PCR_high_stringency.xml", package = "openPrimeR") settings <- read_settings(settings.xml) It reoprt :Due to missing external tools the following constraints were ignored:cross_dimerization,secondary_structure,self_dimerization. But I have already installed MELTING, ViennaRNA ,OligoArrayAux ,MAFFT and Pandoc.

Cheack thesettings@Input_Constraints@status: cross_dimerization, secondary_structure,self_dimerization were seted as FALSE

matdoering commented 2 years ago

If dimerization and secondary structure calculations are not possible this is due to missing executables or incorrect versions for OligoArrayAux and ViennaRNA. To debug your issue, please have a look at the checks that are performed to identify the correct Installation of the tools:

https://github.com/matdoering/openPrimeR/blob/master/R/zzz.R

Most importantl, the tool executables must be in your PATH. If you have issues solving the problem you can also use the docker image of openPrimeR, which contains all dependencies:

https://hub.docker.com/r/mdoering88/openprimer/

YangLeng90 commented 2 years ago

Thank you very much; At your suggestion, I have solved this issue. Another question: Is ther any parameters in XML setting file to set multiplex PCR Amplicon length

matdoering commented 2 years ago

The amplicon length can't be set as an explicit parameter but you can set the allowed binding region for forward and reverse reads in the templates that you have loaded.

YangLeng90 commented 2 years ago

Thank you for you reply When I run: optimal.primers <- design_primers(template.df[1:2,], mode.directionality = "fw", settings = design.settings) It report an error: task 1 failed ,can't open the connection, because it can not find the met_seq**.result.csv I have saw the souce code of con_melting_temperature.R at line 293 result.file <- paste(out.file, ".results.csv", sep = "") but I can't find where to generate this file

matdoering commented 2 years ago

Looks like melting-batch isn't working correctly. Can you check if you can run it independently?

YangLeng90 commented 2 years ago

After installed melting, I can only find melting command and there is no melting-batch, so I create a soft link melting-bach to melting