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kbws_readme [2010/11/19 09:16]
cory
kbws_readme [2014/01/18 07:44] (current)
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-====== KBWS EMBASSY package ver. 1.0.======+====== KBWS EMBASSY package ver. 1.0.======
 KEIO Bioinformatics Web Service (http://​www.g-language.org/​kbws/​) KEIO Bioinformatics Web Service (http://​www.g-language.org/​kbws/​)
  
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 ===== Installation ===== ===== Installation =====
  
-== REQUIREMENT == +=== REQUIREMENT ​=== 
-EMBOSS (> 6.2.0) - This EMBASSY package requires EMBOSS version 6.2.or above.+EMBOSS (> 6.5.7) - This EMBASSY package requires EMBOSS version 6.5.or above.
  
-== INSTALLATION == +=== INSTALLATION ​=== 
-In the following examples, we assume downloaded EMBOSS filename is EMBOSS-6.2.0.tar.gz.+In the following examples, we assume downloaded EMBOSS filename is EMBOSS-latest.tar.gz ​(EMBOSS-6.5.7).
  
-  - Download and compile EMBOSS source code +1. Download and compile EMBOSS source code 
-    % wget ftp://​emboss.open-bio.org/​pub/​EMBOSS/​EMBOSS-6.2.0.tar.gz +    % wget ftp://​emboss.open-bio.org/​pub/​EMBOSS/​EMBOSS-latest.tar.gz 
-      (or curl -O ftp://​emboss.open-bio.org/​pub/​EMBOSS/​EMBOSS-6.2.0.tar.gz) +      (or "curl -O ftp://​emboss.open-bio.org/​pub/​EMBOSS/​EMBOSS-latest.tar.gz"
-    % tar -xzf EMBOSS-6.2.0.tar.gz +    % tar xzf EMBOSS-latest.tar.gz 
-    % cd EMBOSS-6.2.0+    % cd EMBOSS-6.5.7
     % ./configure     % ./configure
     % make     % make
     % sudo make install     % sudo make install
  
-  - Make new directory "​embassy"​ (in EMBOSS-6.2.0/ directory) if it does not exist already+2. Make new directory "​embassy"​ (in EMBOSS-6.5.7/ directory) if it does not exist already
     % mkdir embassy     % mkdir embassy
  
-  - Go into that directory.+3. Go into that directory.
     % cd embassy     % cd embassy
  
-4Place KBWS file in current directory +4Place KBWS file in current directory 
-   ​% wget http://​www.g-language.org/​kbws/​source/​KBWS-1.0.5.tar.gz +    % wget http://​www.g-language.org/​kbws/​source/​KBWS-1.0.9.tar.gz 
-      or +       (or "curl -O http://​www.g-language.org/​kbws/​source/​KBWS-1.0.9.tar.gz")
-     curl -O http://​www.g-language.org/​kbws/​source/​KBWS-1.0.5.tar.gz+
  
-5Uncompress the KBWS tarball package, and go into the new KBWS directory +5Uncompress the KBWS tarball package, and go into the new KBWS directory 
-   % tar xzf KBWS-1.0.5.tar.gz +   % tar xzf KBWS-1.0.9.tar.gz 
-   % cd KBWS-1.0.5 +   % cd KBWS-1.0.9 
-    ( EMBOSS-6.2.0/​embassy/​KBWS-1.0.)+    ( EMBOSS-6.5.7/​embassy/​KBWS-1.0.)
  
-6Configure and compile+6Configure and compile
    % ./configure (use same options as you used to compile emboss)    % ./configure (use same options as you used to compile emboss)
    % make    % make
    % sudo make install    % sudo make install
  
-C) Note+=== Note ===
  
-1) On some systems there may be compatibility problems with different+== libtool problem == 
 +On some systems there may be compatibility problems with different
 automake, autoconf or libtool versions. If a libtool problem automake, autoconf or libtool versions. If a libtool problem
 arises you can try deleting the following files: arises you can try deleting the following files:
- 
    ​config.cache    ​config.cache
    ​ltmain.sh    ​ltmain.sh
    ​ltconfig    ​ltconfig
    ​libtool    ​libtool
- 
 and then type and then type
- 
    % aclocal -I m4    % aclocal -I m4
    % autoconf    % autoconf
    % automake -a    % automake -a
- 
 and then retry make. and then retry make.
  
-2) When you are upgrading EMBOSS, please be sure to uninstall old version of EMBOSS and KBWS. If you override them, some older version of files may cause errors.+== Update of EMBOSS == 
 +When you are upgrading EMBOSS, please be sure to uninstall old version of EMBOSS and KBWS. If you override them, some older version of files may cause errors.
  
-3) If you use "​./​configure"​ command with "​--prefix"​ option, please rewrite "​emboss_acdroot"​ and "​emboss_data"​ value in ~/.embossrc file. Please check "​~/​.embossrc"​ file for further informations.+== EMBOSS is already installed == 
 +When EMBOSS is already installed in your system, please install KBWS at the same PATH as existed EMBOSS by '​--prefix'​ option. 
 + 
 +== Non-root users (using '​--prefix'​ option== 
 +If you use "​./​configure"​ command with "<​nowiki>​--</​nowiki>​prefix"​ option, please rewrite "​emboss_acdroot"​ and "​emboss_data"​ value in ~/.embossrc file. Please check "​~/​.embossrc"​ file for further informations.
  
 ===== QuickStart ===== ===== QuickStart =====
-A) Information of KBWS tools + 
-1) List of all tools+=== DATABASE DEFINITION === 
 +The database definitions for following commands are available at "​KBWS-1.0.9/​data/​embossrc-template"​.  
 + 
 +The latest version is available at following URL: 
 +http://​soap.g-language.org/​kbws/​embossrc 
 + 
 +=== Information of KBWS tools === 
 + 
 +== List of all tools ==
  
 If you want to get list of all tools included in KBWS, you can try If you want to get list of all tools included in KBWS, you can try
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       % wossname -showembassy KBWS       % wossname -showembassy KBWS
  
-2) Documentation+== Documentation ​==
  
 You can view available documentations with "​tfm"​ utility included in EMBOSS. You can view available documentations with "​tfm"​ utility included in EMBOSS.
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       % tfm kblast # example for "​kblast"​       % tfm kblast # example for "​kblast"​
  
-B) Usage example+=== Usage example ​===
  
 Sample files used in this section are available from EMBOSS package. Sample files used in this section are available from EMBOSS package.
-( EMBOSS-6.2.0/​test/​data/​* )+( EMBOSS-6.4.0/​test/​data/​* )
  
-1kblast (BLAST)+1kblast (BLAST)
       % kblast swissprot:​FOXP2_HUMAN -d swissprot -format 8 -eval 1e-100       % kblast swissprot:​FOXP2_HUMAN -d swissprot -format 8 -eval 1e-100
       Search similar sequences in public repositories using BLAST       Search similar sequences in public repositories using BLAST
       Output file [foxp2_human.kblast]:​       Output file [foxp2_human.kblast]:​
-      Jobid: kbws_4981686 
-      ****** 
       ​       ​
       % cat foxp2_human.kblast       % cat foxp2_human.kblast
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-2kcentroidfold (Centroid Fold)+2kcentroidfold (Centroid Fold)
       % kcentroidfold       % kcentroidfold
       RNA 2D structure prediction from an RNA sequence using CentroidFold       RNA 2D structure prediction from an RNA sequence using CentroidFold
       Input (gapped) sequence(s):​ dna.fasta       Input (gapped) sequence(s):​ dna.fasta
 +      Output image file name [kcentroidfold.png]:​
       Output file [fasta.centroidfold]:​       Output file [fasta.centroidfold]:​
-      Jobid: 13401346 + 
-      ​*********** +      ​% ls kcentroidfold.png 
-      ​http://​soap.g-language.org/​result/​13401346.png+      ​kcentroidfold.png
       ​       ​
       % cat fasta.centroidfold       % cat fasta.centroidfold
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       % wget http://​soap.g-language.org/​result/​13401346.png       % wget http://​soap.g-language.org/​result/​13401346.png
  
-3kweblogo (WebLogo)+3kweblogo (WebLogo)
    % kweblogo dna.m-fasta    % kweblogo dna.m-fasta
    make the generation of sequence logos using WebLogo    make the generation of sequence logos using WebLogo
-   Jobid3203930 +   Output file name [kweblogo.png]
-   ** +    
-   http://soap.g-language.org/​alis/​result/​3203930.png+   % ls kweblogo.png 
 +   ​kweblogo.png
  
-C) Sample data+=== Sample data ===
  
 You can use sample data included in EMBOSS. You can use sample data included in EMBOSS.
 Please check test/ directory in EMBOSS package. Please check test/ directory in EMBOSS package.
- 
- 
 ===== Content ===== ===== Content =====
   * gSOAP Toolkit   * gSOAP Toolkit
kbws_readme.1290158162.txt.gz · Last modified: 2014/01/18 07:44 (external edit)