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kbws_readme [2011/04/01 02:15]
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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 === 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-latest.tar.gz (EMBOSS-6.3.1).+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
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       (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-latest.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
  
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 4. Place KBWS file in current directory 4. Place KBWS file in current directory
-    % wget http://​www.g-language.org/​kbws/​source/​KBWS-1.0.7.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-1.0.7.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-1.0.7.tar.gz +   % tar xzf KBWS-1.0.9.tar.gz 
-   % cd KBWS-1.0.7 +   % 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
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 == 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 === === DATABASE DEFINITION ===
-The database definitions for following commands are available at "​KBWS-1.0.7/​data/​embossrc-template"​. ​+The database definitions for following commands are available at "​KBWS-1.0.9/​data/​embossrc-template"​. ​
  
 The latest version is available at following URL: The latest version is available at following URL:
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 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)
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       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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       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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    % 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 ===
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 This EMBASSY package is depended on gSOAP Toolkit to use SOAP This EMBASSY package is depended on gSOAP Toolkit to use SOAP
 transfer, which is included in gsoap/ directory and automatically used during transfer, which is included in gsoap/ directory and automatically used during
-compilation. gSOAP Toolkit is included in the KBWS package.+compilation.
  
 ===== Contact ===== ===== Contact =====
   Kazuki Oshita < cory@g-language.org >   Kazuki Oshita < cory@g-language.org >
     Institute for Advanced Biosciences,​ Keio University.     Institute for Advanced Biosciences,​ Keio University.
kbws_readme.1301624139.txt.gz · Last modified: 2014/01/18 07:44 (external edit)