diff --git a/README b/README
index f36937ec6..7bed41131 100644
--- a/README
+++ b/README
@@ -46,23 +46,36 @@ and DBGET etc.
[RAA:postgres], [RAA:oracle] to use with BioSQL.
* [RAA:bdb] for faster flat file indexing.
* [RAA:pp] for pretty print in debug.
+ * [RAA:soap4r] (version >= 1.4.8.1) for KEGG API. Note that libraries
+ which SOAP4R depends such as [RAA:date2], [RAA:devel-logger],
+ [RAA:http-access] (version >= j) with one of [RAA:xmlscan], [RAA:rexml],
+ [RAA:rexml-stable], [RAA:xmlparser], [RAA:nqxml] are also needed.
+ * If you are using Ruby (version >= 1.8), xmlscan, rexml and date2 are
+ already included in the Ruby installation.
* External applications can be used if installed
- * Blast 2.2.5 or better for local blast execution
- * FASTA for local fasta, ssearch execution
- * HMMER for local hmmsearch, hmmpfam execution
+ * Blast (version >= 2.2.5) for blast execution on local computer
+ * FASTA for fasta, ssearch execution on local computer
+ * HMMER for hmmsearch, hmmpfam execution on local computer
== INSTALL
In the bioruby source directory (such as bioruby-x.x.x/),
+ % ruby extconf.rb
+ % su
+ # make site-install
+
+or
+
% ruby install.rb config
% ruby install.rb setup
+ % su
# ruby install.rb install
-If you are using Mac OS X, last line can be
+If you are using Mac OS X, the last two lines would be
% sudo ruby install.rb install
@@ -75,11 +88,17 @@ for more details.
If you want to use the OBDA (Open Bio Database Access) to obtain database
entries, copy a sample config file
+
etc/bioinfomatics/seqdatabase.ini
+
to
+
/etc/bioinfomatics/seqdatabase.ini (system wide configuration)
+
or
+
~/.bioinformatics/seqdatabase.ini (personal configuration)
+
and chage the contens according to your preference. For more
informations on the OBDA, see (()).
@@ -102,11 +121,11 @@ included in the BioRuby package comes from [RAA:setup] by Minero Aoki.
== AUTHORS
-* KATAYAMA Toshiaki , Project leader
+* KATAYAMA Toshiaki , project leader
* Yoshinori K. Okuji
-* Mitsuteru S. Nakao
+* Mitsuteru C. Nakao
* KAWASHIMA Shuichi
* GOTO Naohisa
- * and some others on the Internet...
+ * and many others on the Internet...