Documentation - Installation.

To install r-make, follow these instructions.


Before running the r-make, the following supporting software must be installed:

     • make (version = 3.82)
     • cmake (version = 2.6.4)
     • gcc (version = 4.4.6)
     • perl (version = 5.10.1)
     • R (version = 2.15.2)
     • rsync (required only if syncing of output to websever is enabled)
     • star (version = 2.3.0)
     • bamtools (version = 2.2.1)
     • bedtools (version = 2.17.0)
     • fastx toolkit (version = 0.0.13)
     • image magick (version = 6.7.6, with PNG delegate)

Remember to setup the appropriate environmental variables,

echo 'export LDFLAGS="$LDFLAGS -L/path/to/bamtools/lib"' >> ~/.bashrc
echo 'export CFLAGS="$CFLAGS -I/path/to/bamtools/include"' >> ~/.bashrc
echo 'export LDFLAGS="/path/to/bamtools/lib:$LD_LIBRARY_PATH"' >> ~/.bashrc
source ~/.bashrc

NOTE: only above listed versions of software have been tested -- other versions may or may not work.

R packages.

After R >= 2.14.1 is installed, install the following R packages:

     • Hmisc
     • gplots
     • RColorBrewer
     • ggplot2
     • limma
     • scales
     • plyr
     • pheatmap
     • car
     • xtable
     • reshape
     • gridExtra
     • GGally
     • ggbio
     • GenomicRanges

To install all packages at once, load up R and type:

install.packages(c("Hmisc", "gplots", "RColorBrewer", "ggplots2",
"scales", "plyr", "pheatmap", "car", "xtable", "reshape",
"gridExtra","GGally"), dependencies = TRUE)
biocLite(c("limma", "ggbio","GenomicRanges"))

Perl modules.

The below perl (version >= 5.10.1) modules need to be installed.

     • File::Find::Rule
     • File::Basename
     • File::Spec
     • File::Copy
     • XML::Simple
     • Data::Dumper

The simplest way to install perl packages is to use the cpanm module. To use the cpanm module, first check that local::lib is installed. If it isn't, download, gunzip, and unpack the local::lib tarball. Then, execute the following commands in the unpacked directory:

perl Makefile.PL --bootstrap
make test && make install

Next, setup the appropriate environmental variables

echo 'eval $(perl -I$HOME/perl5/lib/perl5 -Mlocal::lib)' >>~/.bashrc

Now you can install the App::cpanminus package. To install the package, open cpan,


Then, install the package,

install App::cpanminus

Afterward, to quit cpan, type quit.

Finally, you can install perl modules using cpanm, which is as simple as:

cpanm File::Find::Rule
cpanm XML::Simple
cpanm Data::Dumper
cpanm File::Basename
cpanm File::Spec
cpanm File::Copy
cpanm List::MoreUtils

NOTE: remember to set your PERL5LIB path:

echo 'PERL5LIB=~/perl5/lib/perl5' >>~/.bashrc
echo 'export PERL5LIB' >>~/.bashrc

Installing r-make.

Download, gunzip, and unpack the rmake tarball. Go into the bin directory within the newly created rmake-X.X folder and type 'make':

tar -xzvf rmake-X.X.tgz
cd rmake/bin

NOTE: it is a good idea to create a log of the installation in case of failure; make 2>&1 > make.log

r-make is now installed. Before using it, setup the third-party directory found within the r-make folder. Create symbolic links of the following binaries in the rmake/third-party directory:
     • bamtools
     • bcftools
     • bedtools
     • convert (part of imagemagick)
     • fastx_quality_stats
     • R
     • Rscript
     • samtools
     • star
For example,

ln -s /path/to/<STAR binary> /path/to/r-make-X.X/third-pary/star

Before use, don't forget to download pre-created reference packages.

Installing reference packages.

To install pre-created references packages (including star indexes and annotation files), download download a reference pack and gunzip and unpack in the topmost r-make. For example, if you downloaded the hg19 reference package,

cd rmake-X.X
tar -xzvf hg19.tgz

Validate the installation.

You can validate the installation with a sample dataset provide here.


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p. zumbo