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...