This page was last updated on Friday, 08-Jan-2016 17:13:32 CST
Installation notes for RNAmmer version 1.2
Web interface
Prerequisites
ncompress for extracting the distribution archive
$ sudo apt-get install ncompress
Installation
- Download through web page + email
http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?rnammer
and save in /programinstallers
- $ ver="1.2"
- $ cd /usr/local/bin/
- Convert the compression method to the usual one
$ uncompress -v /programinstallers/rnammer-$ver.src.tar.Z
/programinstallers/rnammer-1.2.src.tar.Z: -- replaced with /programinstallers/rnammer-1.2.src.tar
- $ gzip -9 /programinstallers/rnammer-$ver.src.tar
- Warning, tar bomb!
$ mkdir rnammer && cd rnammer
- $ tar -zxvf /programinstallers/rnammer-$ver.src.tar.gz
RNAMMER requires the older version of hmmsearch (v2).
You can obtain the hmmsearch_v2 at
ftp://selab.janelia.org/pub/software/hmmer/2.3.2/hmmer-2.3.2.tar.gz.
After building the software, we suggest you rename this version of hmmsearch as 'hmmsearch2'.
- I put hmmsearch2 in the /usr/local/bin/rnammer/ directory
- Update hmmsearch location
$ nano /usr/local/bin/rnammer/rnammer
…
my $INSTALL_PATH = "/usr/cbs/bio/srclocal/bin/rnammer-1.2";
…
if ( $uname eq "Linux" ) {
$HMMSEARCH_BINARY = "/usr/cbs/bio/bin/linux64local/bin/rnammer/hmmsearch2"; # version 2.3.2
…
- Install man page
$ gzip man/rnammer.1 && sudo mv man/rnammer.1.gz /usr/share/man/man1/
- Add to default PATH for all users
$ sudo nano /etc/profile
…
PATH="$PATH:/usr/local/bin/rnammer"
…