On Wed, Mar 17, 2010 at 7:15 PM, <[email protected]> wrote: > Hi, > I have been attempting to install Biomart 0.6 on a 64 bit linux machine > and i keep running into all sorts of problems as many of the libraries i > intend to use are 32 bit. > Has anyone been able to successfully do this? Any ideas how i can go about > this please? > I have installed a 32 bit perl (with the recommended tweaking to fool the > system) and but then getting Perl modules via CPAN fails to works and > manual module installation seems rather crude. Here is the error i get > from CPAN > > > YAML Error: Invalid element in map > Code: YAML_LOAD_ERR_BAD_MAP_ELEMENT > Line: 3 > Document: 1 > > CPAN by the way works fine with the 64 bit perl > > Thanks > Nelson > >
I'd suggest installing the latest available Biomart version (Biomart 0.7) instead of Biomart 0.6 unless there is an important reason not to. A month ago I did manage to install Biomart 0.7 on two PCs running 64bit Fedora core 10 and 12 and another server running 64bit Ubuntu (some recent version). It is important follow the installation overview available at "http://www.biomart.org/install-overview.html"; carefully. I find the installation of Perl modules generally more involving compared to the installation of components of other language example jar files for a Java application. That said, I did not find any issues with some modules being only 32bit compatible. This is what I did do. I first installed by manually building from source Apache httpd server in a self contained directory by using --prefix=<some/dir> configuration option of httpd along with other essential options, then I installed mod perl as explained in the "install-overview.html" document. Then I started installing the required and listed Perl modules as per the same document mostly using yum -y install perl-<some-module> for Fedora and CPAN for Ubuntu. Some module could not be easily installed especially on Ubuntu. These hard to install modules required manual search on CPAN (website), download, configure, compile, and install activities. And remember to install the Perl driver for the DB you wish to connect to. Since it seems you may have done some unusual installation of Perl modules, see if you can uninstall them then start off on a clean slate. Allan.
