add todo

[function2gene.git] / README

diff --git a/README b/README
index 182edf7d443bf15fccdabc40752cb906867c3b75..4cb2138ef7e3e44ee4fa2cb7af8ad22b4838e0be 100644 (file)
--- a/README
+++ b/README
@@ -5,11 +5,10 @@ Prerequisites
 Function2Gene requires the following modules and programs to work
 properly:
 
-  * perl
-  * wget
-  * HTML::TreeBuilder
-  * HTML::ElementTable
-  * XML::Parser
+  * 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.
@@ -30,13 +29,14 @@ If you are running Debian, you can just run the following:
 
 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 (a linux-like
-environment for windows), which (by default) will install perl and wget.
+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 above to install the required
-modules:
+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
@@ -44,16 +44,46 @@ modules:
 
 Other Operating Systems
 
-If you are using another operating system (minux, MacOS 9, UNIVAX, Plan9,
-OS/2, etc.) you're on your own.
+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 a bin directory. For a
-demonstration, you can simply do the following:
-
-cd bin;
-echo 'transferrin' > keywords.txt
-function2gene --keywords keywords.txt --results keyword_results;
+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;
+
+which creates a keywords file with a single keyword, transferrin, and
+runs the various subscripts, putting the results in a keyword_results
+directory.