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