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

# Load modules, always specify version number.
$ module load R/4.3.1
$ module load intel-compiler/2021.10.0
$ module load intel-mkl/2023.2.0

# Install glpk under the $HOME/.local directory
$ cd /g/data/z00/mma900/build
$ wget http://ftp.gnu.org/gnu/glpk/glpk-5.0.tar.gz
$ tar -zxvf glpk-5.0.tar.gz
$ cd glpk-5.0
$ ./configure --prefix=$HOME/.local
$ make
$ make install
$ export C_INCLUDE_PATH=$HOME/.local/include:$C_INCLUDE_PATH
$ export LIBRARY_PATH=$HOME/.local/lib:$LIBRARY_PATH
$ export LD_LIBRARY_PATH=$HOME/.local/lib:$LD_LIBRARY_PATHmodule load glpk/5.0

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


# Install RcppTOML package
> q()
Save workspace image? [y/n/c]: n
$ cd /g/data/z00/mma900/build
$ wget https://cran.r-project.org/src/contrib/Archive/RcppTOML/RcppTOML_0.1.7.tar.gz
$ R CMD INSTALL RcppTOML_0.1.7.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)
Loading required package: SeuratObject
Loading required package: sp

Attaching package: ‘SeuratObject’

The following object is masked from ‘package:base’:

    intersect

>


# 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 SNPRelate package
> BiocManager::install("SNPRelate")

# Install muscle
$ cd /g/data/z00/mma900/build
$ wget https://github.com/rcedgar/muscle/archive/refs/tags/5.1.0.tar.gz
$ tar -zxvf 5.1.0.tar.gz
$ cd muscle-5.1.0/src
$ make

# Install phylip for dnaml package
$ cd /g/data/z00/mma900/build
$ wget https://phylipweb.github.io/phylip/download/phylip-3.697.tar.gz
$ tar -zxvf phylip-3.697.tar.gz
$ cd phylip-3.697/src
$ make -f Makefile.unx install

# Install snphylo
$ cd /g/data/z00/mma900/build
$ wget https://github.com/thlee/SNPhylo/archive/refs/tags/20180901.tar.gz
$ tar -zxvf 20180901.tar.gz
$ cd SNPhylo-20180901
$ chmod 755 setup.sh
$ export R_LIBS=/g/data/z00/mma900/build/SNPhylo-20180901/R_LIBS:$R_LIBS
$ ./setup.sh
Version: 20141127

START TO SET UP FOR SNPHYLO!!!

The detected path of R is /apps/R/4.3.1/bin/R. Is it correct? [Y/n] Y
The detected path of python is /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): /g/data/z00/mma900/build/muscle-5.1.0/src/Linux/muscle

dnaml is not found. Is the program already installed? [y/N] y
Please enter the path of dnaml program (ex: /home/foo/bin/dnaml): /g/data/z00/mma900/build/phylip-3.697/exe/dnaml

At least one R package (gdsfmt, SNPRelate, getopt or phangorn) to run this pipeline is not found. Are the packages already installed? [y/N] N
Do you want to install the packages by this script? [y/N] y
...
* DONE (getopt)
...
* DONE (phangorn)

The downloaded source packages are in
	‘/scratch/z00/mma900/tmp/RtmpjiNQkB/downloaded_packages’
Error: With R version 3.5 or greater, install Bioconductor packages using BiocManager; see https://bioconductor.org/install
Execution halted

SNPHYLO is successfully installed!!!

# Test snphylo
$ ./snphylo.sh

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