* Update readme

[function2gene.git] / README

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 INSTALLATION 
 
 INSTALLATION 
 

-Function2Gene currently requires the following:
+Prerequisites

 
 

-perl
-wget
-HTML::TreeBuilder
-HTML::ElementTable
-XML::Parser::Expat
-Thread::Queue
+Function2Gene requires the following modules and programs to work
+properly:

 
 

-these requirements are most easily satisfied on a Debian system (or
-other unix systems) but it is possible to use windows system as well.
+  * 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/

 
 

-On Debian machines:
+The operating system-specific instructions below will help you to
+install these modules.

 
 

-aptitude install wget perl libwww-perl libxml-parser-perl dh-make-perl;
-dh-make-perl --cpan --build --install Thread::Queue;
+Unix instructions

 
 

-will retrieve the necessary commponents. [On lenny or unstable, you
-will want libhtml-parser-perl instead of libwww-perl.]
+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:

 
 

-For other systems, installing the modules using CPAN may be the best
-approach.
+ 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
 
 
 
 USAGE
 

-All of the programs are located within a bin directory. For a
-demonstration, you can simply do the following:
+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
+'keyword<tab>0.3<newline>', 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;

 
 

-cd bin;
-echo 'transferrin' > keywords.txt
-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.