/biomartProbes

command line tool to extract probes information from the ensembl biomart and to export it into a Solr server

Primary LanguageJava

Instructions to install probe-searcher

  1. Get the most updated probes information form biomart using the uploader biomartProbes. This requires to be executed twice, one for uniprot and one for ensemble. > java -jar biomartProbes-1.1.jar FETCH ENSEMBL > java -jar biomartProbes-1.1.jar FETCH UNIPROT

    By executing this commands the folders resultsENSEMBL and resultsUNIPROT will be created and populated with the data from biomart.

  2. Get a solr Instance with the 2 cores up and running. 2.1 untar the solr server > tar xvfz probe_solr.tgz 2.2 Run the server > cd probe_solr > java -jar -Xmx500m start.jar This solr instance has been set up to run in port 8984, but that can be changed in the file probe_solr/etc/jetty.xml Assuming is using localhost, you can check that is running by checking this URL http://localhost:8984/solr/

  3. Load the data into the solr servers using the same biomartProbes tool. > java -jar biomartProbes-1.1.jar UPLOAD resultsENSEMBL/ http://localhost:8984/solr/ensembl2probes > java -jar biomartProbes-1.1.jar UPLOAD resultsUNIPROT/ http://localhost:8984/solr/uniprot2probes You can check it has been loaded by testing this URL http://localhost:8984/solr/ensembl2probes/select?q=*&fq=&start=0&rows=10

  4. Install tomcat > tar xvfz apache-tomcat-7.0.11.tar.gz > cd tomcat/bin > ./startup You can change the port where tomcat will be running editing the file [tomcat]/conf/server.xml it usually runs on port 8080. check http://localhost:8080

  5. Install the DAS server in tomcat. > cp das-srv.war tomcat/webapps/ > cd tomcat/bin > ./shutdown > ./startup

  6. Configure the DAS server editing the file [tomcat]/webapps/das-srv/MydasServerConfig.xml 6.1 Edit the values of the global properties keyphrase and indexerpath: 6.2 For each data source edit the values of the property solr_url 6.3 restart tomcat > ./shutdown > ./startup

  7. Index the DAS datasources by going to the URL http://localhost:8080/das-srv/das/indexer?keyphrase=yes Remeber to update the server/port in case you are using a different one.

  8. Install the website in a web server (e.g. apache) > tar xvfz website.tgz > mv website/* [apache_dir]/probes-search

  9. Edit the 1st line of the javascript file that points to the DAS server: [probes-search]/js/control.js var server_url = 'http://localhost:8081/das-srv/das/';