INSTALLATION Prerequisites Function2Gene requires the following modules and programs to work properly: * perl http://www.perl.org/get.html * HTML::TreeBuilder http://search.cpan.org/dist/HTML-Tree/ * HTML::ElementTable http://search.cpan.org/dist/HTML-Element-Extended/ * XML::Parser http://search.cpan.org/dist/XML-Parser/ The operating system-specific instructions below will help you to install these modules. Unix instructions If you're running a reasonably modern Linux (or other UNIX variant, like MacOS X) you already have perl and wget. If so, you can install the remaining modules by doing the following: cpan install HTML::TreeBuilder cpan install HTML::Element::Extended cpan install XML::Parser If you are running Debian, you can just run the following: aptitude install wget perl libhtml-element-extended-perl libxml-parser-perl Windows If you are using a windows-based machine, first consider switching to (or dual-booting) Debian or Ubuntu or a similar Free Software distribution. If switching isn't for you, you will need to install cygwin (http://www.cygwin.com/) (a linux-like environment for windows), which (by default) will install perl and wget. You can then use the cpan commands listed below to install the required modules (and any needed depependencies): cpan install HTML::TreeBuilder cpan install HTML::Element::Extended cpan install XML::Parser Other Operating Systems If you are using another operating system (minux, MacOS 9, UNIVAX, Plan9, OS/2, etc.) you'll need to refer to your operating system's documentation for information on how to install the required modules. USAGE All of the programs are located within the bin directory of the tarball which is downloadable above. First, change directories to the bin directory (cd bin.) Then create a kewyords file which contains kewyords separated by newlines. You can optionally add a weight for each keyword separated by a tab. (That is, the file will contain lines of 'keyword0.3', for example.) You can do this in any text editor that is capable of saving text files, like vim or emacs. Finally, make a results directory (mkdir keyword_results), and run function2gene with the --keywords option specifying the keywords file that you have created and the --results option specifying the results directory you have created (./function2gene --keywords keywords.txt --results keyword_results.) The results will be in the keyword_results directory in a file called combined_results.txt, and a sumary table will be there as well, called combined_results_table.txt The details of the operation of function2gene are explained in its documentation; type ./function2gene --man; to see it. As a demonstration, you can simply do the following, which creates a keywords.txt file with a single keyword, 'transferrin', and runs the keywords: cd bin; echo 'transferrin' > keywords.txt mkdir keyword_results; ./function2gene --keywords keywords.txt --results keyword_results; which creates a keywords file with a single keyword, transferrin, and runs the various subscripts, putting the results in a keyword_results directory.