Installing BioPerl on SuSE

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For the generic instructions, see: Installing BioPerl on Unix.

Installing BioPerl on SLES9 or SuSE-9.3

Since I wrote this back in 2006, bioperl-1.6 has improved things enormously, SLES9 is even more out of date. The easiest path forward is to upgrade to SLES11 or openSuSE11.2, then have a look at the non-perl prerequisites and use yast2 to install them from provided RPMs Then CPAN> install CJFIELDS/BioPerl-1.6.1.tar.gz (Or whatever the latest version is)


This is only relevant if you're stuck installing on SLES9. I'll probably delete it soon. (now = 2010-04-01)

First let it be said, Bioperl is bigger than Beh Hur and there's bound to be casualties. CPAN does NOT just slip through reams of sucessfull installs, there's errors and optional prerequisites.

There is evidence of a lot of work going on, but not all the TODOs have been shaken out.

I just wish they listed their pre-requisites more comprehensively and allowed a "follow" CPAN policy to do the work.

My desk is littered with lists of modules that didn't get installed automatically but were needed for full functionality.

Getting there is a tortuous path, let's start:

SLES9 users have a bit of catching up to do first:

   SLES9 is based on SuSE9.1 and is pretty outdated these days (2006-05-11)
   You'll need better versions of the GD libraries than SLES9 provides.
   These RPMs from SuSE 9.3 can be installed,
       gd-2.0.32-6.2
       gd-devel-2.0.32-6.2
           # You may need some of these 9.3 RPMs to get RPM prerequisites satisfied:
           gdbm-devel is needed by gd-2.0.32-6.2
           ncurses-devel is needed by gd-2.0.32-6.2
           syslogd is needed by gd-2.0.32-6.2
           texinfo is needed by gd-2.0.32-6.2
           zlib-devel is needed by gd-2.0.32-6.2
           fontconfig-devel is needed by gd-2.0.32-6.2
           freetype2-devel is needed by gd-2.0.32-6.2
           libjpeg-devel is needed by gd-2.0.32-6.2
           libpng-devel is needed by gd-2.0.32-6.2
           xorg-x11-devel is needed by gd-2.0.32-6.2
   The better GD libs need a better perl wrapper than the SUSE RPM  "perl-GD".
   CPAN install using;   root> perl -MCPAN -e shell   
       install GD         # Should go on with some warnings
       install GD::SVG    # It will fail, there are 2 duff tests 17 and 47
           Easy fix, use: force install
           Otherwise, look GD::SVG
               make test    # The failed tests relate to unexpected returns from obscure uses of "polygon"
               vi t/1.t and disable them  (cook it till they succeed)
               make install
               ^D out of "look"

For all platforms, CPAN install using; root> perl -MCPAN -e shell

   Ace
   Clone
   IO::Scalar
   Test::Pod
   Test::Pod::Coverage
   Tie::IxHash
   Tree::XPathEngine
   Unicide::Map8
   Unicode::String
   XML::DOM::XPath
   XML::Handler::YAWriter
   XML::Filter::BufferText
   XML::XPath
   
   XML::SAX::Writer   # Trouble here
       Failed test (t/05basic.t at line 51)
           iconv converter for real encoding isn't a 'Text::Iconv' it's a 'Text::IconvPtr'
           Well maybe it should be, look and edit or use force.
   install Bundle::BioPerl

It happened? Good. You think your done? WRONG!

Bundle::BioPerl isn't BioPerl with all the trimmings, it's the pre-requisites that bioperl (lowercase) should have demanded.

That was the easy part, now for bioperl itself.

Going into CPAN and saying "install B/BI/BIRNEY/bioperl-1.4.tar.gz" would be too easy, well actually it would blow up in your face with more errors than you would want to track down to assure yourself they were harmless.

So we have to choose between the slack way and the hard way.

Slack: CPAN install and damn the torpedoes!

   force install B/BI/BIRNEY/bioperl-1.4.tar.gz
   I had a boss once who used:    root> make install | grep FATAL
   No output? A perfect compilation/installation!
   He was very productive, but of what was debated.

Not really that hard:

   Abandon bioperl-1.4 like the developers; bioperl-1.5 is the happening place.
   Get it from:
   http://bioperl.org/DIST/current_core_unstable.tar.bz2
   bzcat current_core_unstable.tar.bz2 | tar xvf -
   cd bioperl-1.5.1
   perl Makefile.PL
   make
   make test    # Still 1 error
      # now DB.t test 24 gets 30 results not 28.
      # It's fixed in the CVS version.
   make install    # I don't mind ignoring errors when I know they are harmless.

Hurrah it's on, peace and happyness? Not completely....

You may have seen whinging about Bio::SeqIO::staden::read.pm not being installed properly, it's part of bioperl-ext and you'll wish you had it but that's another story

Installing BioPerl-ext

With bioperl-ext the story is reversed. Having just installed bioperl-1.5.x you'd think you wanted bioperl-ext-1.5 but it really doesn't have a testing suite yet. (as at 2006-06-02)

So we're back to bioperl-ext-1.4

You're not going to get the useful bit (SeqIO) without the staden "io_lib" libraries.

So off to

   http://sourceforge.net/projects/staden  or more specifically
   http://sourceforge.net/project/showfiles.php?group_id=100316

Compile and install, It seems to compile. I used ./configure --prefix=/opt/io_lib/


You can get bioperl-ext-1.4 in CPAN so lets:

   root> perl -MCPAN -e shell
   install B/BI/BIRNEY/bioperl-ext-1.4.tar.gz   It doesn't work.
   look B/BI/BIRNEY/bioperl-ext-1.4.tar.gz
       cd into BioSeqIO/staden
       make test  The problem seems to centre around "undefined symbol: deflateInit2_"

Haven't got it to work yet, let me know if you have solved this.

DON'T just ignore the failed tests and "make install" UNLESS YOU ARE PREPARED TO BLOW THE WHOLE Bio modules directory out of perl and start again!

You want to ignore the warning?

   make install?
   now cd back to bioperl-1.5.1
   try make test again? Not good eh?

Hardly even $.02 worth eh? michaelj

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