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INSTALL
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INSTALL
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Installation Instructions for Package rBLAST
1. Required R packages
From CRAN:
install.packages(c("proxy", "ape"))
From Bioc:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("Biostrings")
BiocManager::install("seqLogo")
BiocManager::install("pwalign")
2. External Software
Linux (Ubuntu/Debian)
====================
Run:
sudo apt-get install clustalw kalign mafft muscle boxshade ghostscript
For other distributions, use the appropriate package manager.
OS X
====
* ClustalW: Install clustalw from http://www.clustal.org/.
* Kalign: Install from https://github.com/TimoLassmann/kalign
* MAFFT: Install from http://mafft.cbrc.jp/alignment/software/.
* MUSCLE: Install from http://www.drive5.com/muscle/.
* Boxshade is currenly not available as an executable (you can download it from http://boxshade.sourceforge.net/ and compile it with the free pascal compiler and install ghostscript).
Windows
=======
* ClustalW: Install clustalw from http://www.clustal.org/.
* Kalign: Needs to be built from https://github.com/TimoLassmann/kalign
* MAFFT: Download ‘mafft.exe’ from http://www.tcoffee.org/Packages/Binaries/windows/.
* MUSCLE: Install from http://www.drive5.com/muscle/.
* Boxshade is currenly not available for Windows
Setting the PATH variable for Windows
* From the Desktop, right-click My Computer and click Properties.
* Click Advanced System Settings link in the left column.
* In the System Properties window click the Environment Variables button.
* Add the folder(s) with the executables to the PATH variable (separated by ;)
* Restart your R session.
* Try the following in R: Sys.which("clustalw") This should show you where it found the executable