In Chebuu/Design-Group-Specific-Primers:

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

Installing OligoArrayAux from U. Albany

The program OligoArrayAux

[http://mfold.rna.albany.edu/?q=DINAMelt/OligoArrayAux][http://mfold.rna.albany.edu/?q=DINAMelt/OligoArrayAux]

is used by the Bioconductor package DECIPHER to predict hybridization efficiency.
It must be installed in a location accessible by the system.

Installing from source

If you're not on Linux or Windows you will need to install OligoArayAux from the compressed source code, which should be a tarball titled something like:

oligoarrayaux-3.8.tar.gz

To installing from source, download and extract the tarball and run Make:

```{bash install_source, eval=F}

cd oligoarrayaux

./configure make sudo make install

### Confirm the installation
To confirm that **OligoArrayAux** is installed and accessible, execute the following R command.            

```r
system("hybrid-min -V")

It should print the installed OligoArrayAux version (currently 3.8 as of Aug. 2020):

hybrid-min (OligoArrayAux) 3.8
By Nicholas R. Markham and Michael Zuker
Copyright (C) 2006
Rensselaer Polytechnic Institute
Troy, NY 12810-3590 USA

That's all

Your DECIPHER installation will now have access to it's dependency OligoArrayAux upon importation:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("DECIPHER")

library(DECIPHER)

More Help

See the DECIPHER docs

The code in this document was basically copied from the Note sections DECIPHER reference manual, available in PDF here:
https://bioconductor.org/packages/release/bioc/html/DECIPHER.html

You can also pull up the docs in RStudio if you hav DCIPHER installed

# Within an RStudio session
?DECIPHER::DesignProbes

UNAFold deprecation warning

Starting November 1, 2020 the U. Albany web server "UNAFold" will change hosts. The UNA Fold server distributes the latest release of OligoArrayAux, and I'm don't know where the site is moving, so I've packaged the oligoarrayaux-3.8 source code and a Windows executable within DesignGroupSpecificPrimers:

system.file('library/oligoarrayaux-3.8.tar.gz', DesignGroupSpecificPrimers)
system.file('library/OligoArrayAux-3.8.exe', DesignGroupSpecificPrimers)

Chebuu/Design-Group-Specific-Primers documentation built on Aug. 17, 2020, 1:29 a.m.