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# Unload modules
$ module unload R intel-compiler intel-mkl

# Load modules, always specify version number.
$ module load R/4.1.0
$ module load intel-compiler/2021.2.0
$ module load intel-mkl/2021.2.0

# Install Biobase, NMF and irlba packages
$ R
> if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
> BiocManager::install("Biobase")
> install.packages("NMF",repos="http://cran.ms.unimelb.edu.au/")
> install.packages("irlba",repos="http://cran.ms.unimelb.edu.au/")

# Install igraph package
> q()
Save workspace image? [y/n/c]: n
$ wget http://igraph.org/nightly/get/r/igraph_1.0.1.tar.gz
$ R CMD INSTALL igraph_1.0.1.tar.gz


# Now you can install Seurat package

# Install Seurat package
$ R
> install.packages("Seurat",repos="http://cran.ms.unimelb.edu.au/")

# Test Seurat
> library(Seurat)
Attaching SeuratObject
>


# All the above packages, except Seurat, are required to install
# the following packages

# Install phangorn package
> install.packages("phangorn",repos="http://cran.ms.unimelb.edu.au/")

# Install gdsfmt package
> q()
Save workspace image? [y/n/c]: n
$ wget https://cran.r-project.org/src/contrib/Archive/gdsfmt/gdsfmt_1.1.0.tar.gz
$ R CMD INSTALL gdsfmt_1.1.0.tar.gz

# Install SNPRelate package
$ wget https://cran.r-project.org/src/contrib/Archive/SNPRelate/SNPRelate_0.9.19.tar.gz
$ R CMD INSTALL SNPRelate_0.9.19.tar.gz

# Install muscle
$ wget http://www.drive5.com/muscle/downloads3.6/muscle3.6_src.tar.gz
$ tar -zxvf muscle3.6_src.tar.gz
$ cd muscle3.6_src # For my case it was pointing to "/short/z00/mma900/build/muscle3.6_src" directory
$ make

# Install phylip for dnaml package
$ cd ..
$ wget http://evolution.gs.washington.edu/phylip/download/phylip-3.696.tar.gz
$ tar -zxvf phylip-3.696.tar.gz
$ cd phylip-3.696 # For my case it was pointing to "/short/z00/mma900/build/phylip-3.696" directory
$ cd src
$ make -f Makefile.unx install

# Install snphylo
$ cd ../..
$ wget http://chibba.pgml.uga.edu/snphylo/snphylo.tar.gz
$ tar -zxvf snphylo.tar.gz
$ cd SNPhylo
$ chmod 755 setup.sh
$ setup.sh

The detected path of R is /apps/R/3.4.0/bin/R. Is it correct? [Y/n] Y
The detected path of python is /usr/bin/python. Is it correct? [Y/n] Y
muscle is not found. Is the program already installed? [y/N] y
Please enter the path of muscle program (ex: /home/foo/bin/muscle): /short/z00/mma900/build/muscle3.6_src/muscle
The detected path of dnaml is /g/data1/gh6/modules/phylip-3.696/exe/dnaml. Is it correct? [Y/n] n
dnaml is not found. Is the program already installed? [y/N] y
Please enter the path of dnaml program (ex: /home/foo/bin/dnaml): /short/z00/mma900/build/phylip-3.696/exe/dnaml

# Test snphylo
$ ./snphylo.sh

# Test phangorn
$ R
> library(ape)
> library(phangorn)
>

# Test Seurat
> library(Seurat)
Attaching SeuratObject
>