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WebLab System Extending

This page tells you how to do some extension on the basic local set-up WebLab system.

Add Databases for Some Services

Add Databases for Some Services
For program services like blast, e-PCR and isPCR , we only provide one database for each program in our distributed WebLab system. The following section tells you how to add databases for these program services.
- blast database
  - For blast program services(blastn, blastp, blastx, tblastn and tblastx), we require you put database files under
    "worker"/data/blastdb directory.
  - Use formatdb program to build your own database files. You can check the man page of formatdb for the detailed information.
  - Modify the configuration file for corresponding programs. For example, if you build nucleic acid blast database refseq_rna, you will have severl refseq_rna.* files under "worker"/data/blastdb directory. Then you have to change the $CATALINA_BASE/WEB-INF/conf/weblab/program/dispatch/ncbi_tools/blastn.xml if you want to add refseq_rna to blastn program service.
    ......
    <param mandatory="true" type="meta_input">
    <name>database</name>
    <label>Choose database</label>
    <arg>-d</arg>
    <comment>Choose databases for searching </comment>
    <format>weblab:metadata:blastdb:nucleotide</format>
    <options>
    <option label="Arabidopsis thaliana genome" value="A_thaliana_genome" selected="true"/>
    <option label="Reference mRNA sequences (refseq_rna)" value="refseq_rna" selected="false"/>
    </options>
    </param>
    ......
  - Restart the Tomcat server to make the modification in effect.
- forward e-PCR database
  - For forward e-PCR program services, we require you put database files under
    "worker"/data/e-PCR/forward directory.
  - Get your database files like UniSTS database.
  - Modify the $CATALINA_BASE/WEB-INF/conf/weblab/program/dispatch/dispatch/ePCR/forward_ePCR.xml. For example, if you want to add UniSTS database to forward e-PCR program service. You will have UniSTS.sts file under "worker"/data/e-PCR/forward directory. Change the configuration file as follow;
    ......
    <param mandatory="true" type="string">
    <name>database</name>
    <label>Choose database</label>
    <arg>-b</arg>
    <comment>Choose databases for searching </comment>
    <options>
    <option label="dbsts" value="dbsts" selected="true"/>
    <option label="genethon" value="genethon" selected="false"/>
    ......
    <option label="UniSTS" value="UniSTS" selected="false"/>
    </options>
    </param>
    ......
  - Restart the Tomcat server to make the modification in effect.
- reverse e-PCR database
  - For reverse e-PCR program services, we require you put database files under
    "worker"/data/e-PCR/reverse directory.
  - Build your database files using famap and fahash programs in e-PCR package. Check the README.txt file of e-PCR for detailed instructions.
  - Modify the $CATALINA_BASE/WEB-INF/conf/weblab/program/dispatch/dispatch/ePCR/reverse_ePCR.xml. For example, if you want to add C_elegans_genome database to reverse e-PCR program service. You will have C_elegans_genome.famp and C_elegans_genome.hash files under "worker"/data/e-PCR/reverse directory. Change the configuration file as follow;
    ......
    <param mandatory="true" type="meta_input">
    <name>dataset</name>
    <label>Choose dataset</label>
    <arg>-S</arg>
    <format>weblab:metadata:reElectronicPCRdb</format>
    <comment>Choose databases for searching </comment>
    <options>
    <option label="Populus_trichocarpa transcripts" value="P_trichocarpa_transcripts" selected="true"/>
    <option label="Caenorhabditis elegans genome" value="C_elegans_genome" selected="false"/>
    </options>
    </param>
    ......
  - Restart the Tomcat server to make the modification in effect.
- isPCR database
  - For isPCR program services, we require you put database files under
    "worker"/data/e-PCR/isPCR directory.
  - Get your database file in fasta format.
  - Modify the $CATALINA_BASE/WEB-INF/conf/weblab/program/dispatch/dispatch/isPCR/isPcr.xml. For example, if you want to add C_elegans_genome database to isPCR program service. You will have C_elegans_genome.fasta files under "worker"/data/isPCR directory. Change the configuration file as follow;
    ......
    <param mandatory="true" type="string">
    <name>database</name>
    <label>database</label>
    <arg>-database</arg>
    <comment>The sequence database to search </comment>
    <options>
    <option label="Arabidopsis thaliana genome" value="A_thaliana_genome" selected="true"/>
    <option label="Caenorhabditis elegans genome" value="C_elegans_genome" selected="false"/>
    </options>
    </param>
    ......
  - Restart the Tomcat server to make the modification in effect.