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

1. Download through web page + email http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?rnammer and save in /programinstallers
2. $ ver="1.2"
3. $ cd /usr/local/bin/
4. 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
5. $ gzip -9 /programinstallers/rnammer-$ver.src.tar
6. Warning, tar bomb!
   $ mkdir rnammer && cd rnammer
7. $ tar -zxvf /programinstallers/rnammer-$ver.src.tar.gz

8. 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'.

9. I put hmmsearch2 in the /usr/local/bin/rnammer/ directory
10. 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
    …
11. Install man page
    $ gzip man/rnammer.1 && sudo mv man/rnammer.1.gz /usr/share/man/man1/
12. Add to default PATH for all users
    $ sudo nano /etc/profile
    …
    PATH="$PATH:/usr/local/bin/rnammer"
    …