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The installation was tested under Linux Ubuntu 9.10.

Installation of NEXT-RNAi

Latest NEXT-RNAi source release can be downloaded from the public github repository

cd
mkdir nextRNAi; cd nextRNAi
git clone https://github.com/boutroslab/nextrnai.git git   

Installation of Bowtie

Bowtie can be downloaded from the Bowtie webpage. Depending on the CPU Bowtie is available for 64bit computers (bowtie-x.x.x-linux-x86_64.zip) or 32bit computers (bowtie-x.x.x-linux-i386.zip).
Bowtie just needs unpacking. NEXT-RNAi requires the bowtie script, and the bowtie-build script for building custom Bowtie libraries / indices.

unzip bowtie-x.x.x-linux-x.zip

Installation of primer3

Primer3 can be downloaded from the Primer3 release page. It is recommended to use version 1.1.4 (file primer3-1.1.4.tar.gz), the latest versions are still in alpha/beta testing.
Primer3 needs to be unpacked and compiled (compilation requires prior installation of a gcc compiler, e.g. included in 'build-essential' package in Ubuntu). NEXT-RNAi requires the primer3_core script located in the src folder.

tar -xvzf primer3-1.1.4.tar.gz
cd source
make all

For Ubuntu primer3 is also available for installation via apt-get:

sudo apt-get install primer3

Installation of mdust

Mdust can be downloaded via this link.
Mdust needs to be unpacked and compiled (compilation requires prior installation of a gcc compiler, e.g. included in 'build-essential' package in Ubuntu). NEXT-RNAi requires the mdust script located in the unpacked folder after compilation.

tar -xvzf mdust.tar.gz
cd mdust
make

Installation of Blat

Download the blat suite available for Linux.
Unpack the blat suite. NEXT-RNAi requires the blat script for alignments with flat-file FASTA databases or gfServer, gfClient and faToTwoBit scripts for alignments using a blat server.

unzip blatSuite.34.zip

Installation of BLAST

Download latest BLAST executables (blast-2.2.x-ia32-linux.tar.gz) from NCBI here.
Unpack the file. NEXT-RNAi requires the blastall script, and the formatdb script for building a BLAST index (both located in the bin folder).

tar -xvzf blast-2.2.x-ia32-linux.tar.gz

For Ubuntu BLAST is also available for installation via apt-get:

sudo apt-get install blast2

Installation of Vienna RNA Package

Download the latest Vienna RNA Package (ViennaRNA-x.x.x.tar.gz) here.
Unpack the file. In the created folder run ./configure, make and sudo make install to make the package (requires prior installation of a gcc compiler, e.g. included in 'build-essential' package in Ubuntu). NEXT-RNAi requires the RNAfold.pl perl script located in the Perl folder.

tar -xvzf ViennaRNA-x.x.x.tar.gz
cd ViennaRNA-x.x.x
./configure
make
sudo make install
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