The installation was tested under MAC OS X (10.5.x, Intel CPU)
Installation of NEXT-RNAi
NEXT-RNAi can be downloaded here and just needs to be unpacked.
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-macos-10.5-x86_64.zip) or 32bit computers (bowtie-x.x.x-macos-10.5-i386.zip).
Bowtie just needs unpacking. NEXT-RNAi requires the bowtie script, and the bowtie-build script for building custom Bowtie libraries / indices.
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-OSX.tar.gz). Version 1.1.1 was found with a bug in the output and the latest versions are still in alpha/beta testing.
Primer3 just needs unpacking. NEXT-RNAi requires the primer3_core script located in the unpacked src folder.
Installation of mdust
Mdust can be downloaded via this link.
Unpack the file. In the folder created open fastafile.c and delete the third line #include <malloc.h> (malloc.h is not needed under Mac OS X, but leads to an error with make). Finally type make (ignore warnings) which creates the mdust script required by NEXT-RNAi (compilation requires prior installation of Apple Developer Tools / Xcode).
Installation of Blat
Download the blat suite available for Intel Macs or Power PCs.
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.
Installation of BLAST
Download latest BLAST executables (blast-2.2.x-universal-macosx.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).
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 Apple Developer Tools / Xcode). NEXT-RNAi requires the RNAfold.pl perl script located in the Perl folder.