Category Archives: rnammer

RNAmmer 1.2 install issues

RNAmmer is getting on in years, but it is still heavily used, something that we, the authors deeply appreciate. However, it is not always easy to install. Here, I describe what needs to be done in order to get it up and running.

Path changes

The changes that have to be introduced are to be found in this section:

## PROGRAM CONFIGURATION BEGIN

# the path of the program
my $INSTALL_PATH = "/usr/cbs/bio/src/rnammer-1.2";

# The library in which HMMs can be found
my $HMM_LIBRARY = "$INSTALL_PATH/lib";
my $XML2GFF = "$INSTALL_PATH/xml2gff";
my $XML2FSA = "$INSTALL_PATH/xml2fsa";

# The location of the RNAmmer core module
my $RNAMMER_CORE     = "$INSTALL_PATH/core-rnammer";

# path to hmmsearch of HMMER package
chomp ( my $uname = `uname`);
my $HMMSEARCH_BINARY;
my $PERL;
if ( $uname eq "Linux" ) {
        $HMMSEARCH_BINARY = "/usr/cbs/bio/bin/linux64/hmmsearch";
        $PERL = "/usr/bin/perl";
} elsif ( $uname eq "IRIX64" ) {
        $HMMSEARCH_BINARY = "/usr/cbs/bio/bin/irix64/hmmsearch";
        $PERL = "/usr/sbin/perl";
} else {
        die "unknown platform\n";
}

The program was in the first place written to be run on the servers at the Danish Technical University, hence the $INSTALL_PATH setting. This should be set to wherever you keep your RNAmmer installation. In my case, I am setting it to /home/karinlag/projects/rnammer, since I am here having it as a local install in my home directory.

The next thing that has to be done, is to get the right HMMer installation and to figure out where perl is.

You will need version 2.3 of HMMer, which you can download from this location. Download it, and read the INSTALL instructions. It should install cleanly on most *nix systems.

I installed hmmer-2.3 in /home/karinlag/src, where it created the directory hmmer-2.3. Inside the src directory you will find the hmmsearch program. Set the $HMMSEARCH_BINARY variable to point to the hmmsearch program. Note: you need to check what the command uname tells you to figure out what system you have so that you know which of the if clauses to modify things in. If it does not say Linux or IRIX64 (which is unlikely these days), you will need to set either the Linux string or the IRIX64 string to what you have, and set the paths below accordingly.

You also need to check that you have the right perl path. You can figure that out by doing ‘which perl’.

You should now be able to do

perl rnammer -S bac -m lsu,ssu,tsu -gff - example/ecoli.fsa

and get results.

Posix errors

You may end up with errors that say something along the lines of 

FATAL: POSIX threads support is not compiled into HMMER; --cpu doesn't have any effect

If you get this, you need to find the following in the core-rnammer script:

system sprintf('%s --cpu 1 --compat ...... and so on

Remove the two instances of –cpu 1 (not the whole sentence, just ‘–cpu 1’), and you should be good to go.

XML/Simple.pm

You might end up with having RNAmmer complain about not being able to find XML/Simple.pm in @INC. To solve this, you need to install perl-XML-Simple. Installing perl modules is something I consider to be deep voodoo, so I won’t even try to describe how to do that. Refer to your system to figure that one out.

Other errors?

If you discover other errors than those I have described here, let me know in the comments!