User Tools

Site Tools


kbws_readme

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision
Previous revision
kbws_readme [2011/01/18 07:24]
cory
kbws_readme [2013/03/08 09:04]
cory [QuickStart]
Line 1: Line 1:
-====== 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/​)
  
Line 22: Line 22:
  
 === 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-6.3.1.tar.gz.+In the following examples, we assume downloaded EMBOSS filename is EMBOSS-latest.tar.gz ​(EMBOSS-6.5.7).
  
 1. Download and compile EMBOSS source code 1. Download and compile EMBOSS source code
     % wget ftp://​emboss.open-bio.org/​pub/​EMBOSS/​EMBOSS-latest.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-latest.tar.gz"​)       (or "curl -O ftp://​emboss.open-bio.org/​pub/​EMBOSS/​EMBOSS-latest.tar.gz"​)
-    % tar -xzf EMBOSS-6.3.1.tar.gz +    % tar xzf EMBOSS-latest.tar.gz 
-    % cd EMBOSS-6.3.1+    % cd EMBOSS-6.5.7
     % ./configure     % ./configure
     % make     % make
     % sudo make install     % sudo make install
  
-2. Make new directory "​embassy"​ (in EMBOSS-6.3.1/ 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
  
Line 43: Line 43:
  
 4. Place KBWS file in current directory 4. Place KBWS file in current directory
-    % wget http://​www.g-language.org/​kbws/​source/​KBWS-1.0.6.tar.gz +    % wget http://​www.g-language.org/​kbws/​source/​KBWS-1.0.9.tar.gz 
-       (or "curl -O http://​www.g-language.org/​kbws/​source/​KBWS-1.0.5.tar.gz"​)+       (or "curl -O http://​www.g-language.org/​kbws/​source/​KBWS-1.0.9.tar.gz"​)
  
 5. Uncompress the KBWS tarball package, and go into the new KBWS directory 5. Uncompress the KBWS tarball package, and go into the new KBWS directory
-   % tar xzf KBWS-1.0.6.tar.gz +   % tar xzf KBWS-1.0.9.tar.gz 
-   % cd KBWS-1.0.6 +   % cd KBWS-1.0.9 
-    ( EMBOSS-6.3.1/​embassy/​KBWS-1.0.)+    ( EMBOSS-6.5.7/​embassy/​KBWS-1.0.)
  
 6. Configure and compile 6. Configure and compile
Line 79: Line 79:
  
 == Non-root users (using '​--prefix'​ option) == == Non-root users (using '​--prefix'​ option) ==
-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.+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 =====
 +
 +=== 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 === === Information of KBWS tools ===
Line 101: Line 107:
  
 Sample files used in this section are available from EMBOSS package. Sample files used in this section are available from EMBOSS package.
-( EMBOSS-6.3.1/​test/​data/​* )+( EMBOSS-6.4.0/​test/​data/​* )
  
 1. kblast (BLAST) 1. kblast (BLAST)
Line 107: Line 113:
       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
Line 135: Line 139:
       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
Line 149: Line 154:
    % 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
  
 === Sample data === === Sample data ===
Line 157: Line 163:
 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.txt · Last modified: 2014/01/18 07:44 (external edit)