latest news

07.17.2017

Documentation outlining our RNA-Seq schema.

schema ...

repo structure ...

qc metrics ...

03.27.2017

PIVOT released (replacing IDV); an extensive R-based GUI for the visualization and analysis of RNASeq data.

access info ...

11.09.2016

PESS has been released and is available for download with source code.

access info ...

03.02.2016

VERSE RNASeq quantifier has been released and is available for download.

access info ...

CRIMSON

Download Oracle data dump: Oracle Dump (29 GB)

The dump was successfully loaded into the following Oracle database:
   Oracle Database 11g Enterprise Edition Release 11.2.0.1.0 - 64bit Production
   With the Partitioning, OLAP, Data Mining and Real Application Testing options

PREPARING DATA FILES:

  • The data dump needs to be extracted from the tar file. This will create a directory called "oracle.dump". The data files (*.dmp) are compressed with bzip2. You must uncompress them prior to loading them into Oracle, using bunzip2. The uncompressed data files will take about 2 TB of disk space. You will need another 2 TB of disk space for the data within the Oracle database. Once loaded into Orace, the oracle.dump directory can be deleted.
  • [oracle@o1 ~]$ tar xvf oracle.dump.tar; cd oracle.dump; bunzip2 *.bz2

LOADING DATA FILES INTO ORACLE:

  • Set DB_CREATE_FILE_DEST, if necessary, specifying where data will go
  • SQL> alter system set DB_CREATE_FILE_DEST = '{location for Oracle managed datafiles}' scope=both;
  • See the result with:
  • SQL> show parameters db_create;
  • Load the create_cipress_tablespace.sql file to create the CIPRES tablespaces. Since the sizes were not specified, they are 100MB each, autoextend on, no max limit.
  • SQL> start create_cipress_tablespace;
  • Specify the location of the data dump
  • SQL> create directory imp_dir as '{directory with data dump}';
  • Load READONLY dataset
  • oracle@o1 ~]$ impdp DIRECTORY=imp_dir DUMPFILE=export_srb3_READONLY_CIPRES_12-01-2009_22935.dmp LOGFILE=import-readonly.log
  • Load CIPRES dataset
  • oracle@o1 ~]$ impdp DIRECTORY=imp_dir DUMPFILE=export_srb3_cipres_11-18-2009_15511_1_01.dmp, export_srb3_cipres_11-18-2009_15511_2_01.dmp, export_srb3_cipres_11-18-2009_15511_3_01.dmp, export_srb3_cipres_11-18-2009_15511_4_01.dmp, export_srb3_cipres_11-18-2009_15511_5_01.dmp, export_srb3_cipres_11-18-2009_15511_6_01.dmp, export_srb3_cipres_11-18-2009_15511_7_01.dmp, export_srb3_cipres_11-18-2009_15511_8_01.dmp, export_srb3_cipres_11-18-2009_15511_9_01.dmp, export_srb3_cipres_11-18-2009_15511_10_01.dmp LOGFILE=import-cipres.log

Web Access

It is not necessary to use a web proxy to access the Oracle database. However if you wish to use a web proxy, one has been included below ("DatabaseProxy.php"). To open an Oracle database connection using a web proxy, include the proxy's URL as the database server (eg 'http://{your website}/DatabaseProxy.php'), with a blank username and password. From the Crimson command line, this can be done using the following commands:
      >>> setDBType("oracle")
      >>> openDatabase("", "", "http://{your website}/DatabaseProxy.php")
The following web proxy only allows for read-only access to the CIPRES database.

Web Proxy For Oracle Database (DatabaseProxy.php)

    <?php
    
    /*
     * Created on March 28, 2006 Henry Jaime
     *
     * Database proxy to return a list of specific values
     * NOTE: must modify results to return specific columns
     */
    
    // THESE MUST BE DEFINIED
    $OracleSID = '';
    $OracleReadOnlyUserID = '';
    $OracleReadOnlyPasswd = '';
    
    define('DB_SID', $OracleSID);
    $DB_USER = trim($_POST['user']);
    $DB_PASS = $_POST['passwd'];
    
    // if 'user' is empty, then use defaults above
    if (empty($DB_USER)) {
      $DB_USER = $OralceReadOnlyUserID;
      $DB_PASS = $OracleReadOnlyPasswd;
    }
    
    $iDBConn = OCILogon($DB_USER, $DB_PASS, DB_SID) or die ("Could not connect.");
    
    executeSql("alter session set current_schema=cipres");
    
    //the sql statement must be the first statement to avoid compound statement sql injection
    define('DB_SQL', $_POST['sql']);
    list($sql, $other) = split(";", DB_SQL);
    
    //only execute SELECT statements; optionally you can limit to specific tables for insert/delete
    if (strpos(strtoupper($sql), 'SELECT') !== false) {
      //filter out malicious code here...
      //allow alpanumeric, space, - = * .
      $sql = preg_replace("/[^= .*a-zA-Z0-9'(,)_-]+/", "", $sql);
      
      executeSql($sql);
    }
    
    return;
    
    function executeSql($sql) {
      global $iDBConn, $iStatement;
      
      $iStatement = @OCIParse($iDBConn, $sql);
      @OCIExecute($iStatement, OCI_DEFAULT);
      
      $arrError = OCIError($iStatement);
      
      if ($arrError['code']) {
    	print $arrError['message'];
    	exit;
      }
      
      $nrows = ocifetchstatement($iStatement, $results,0,-1,OCI_FETCHSTATEMENT_BY_ROW);
      // this will return one row of values per line with either
      // column delimited by ';'.  It is assumed that the calling
      // function knows the order of the columns and the column IDs.
      foreach (array_values($results) as $data) {
    	while (list($key,$value) = each($data)) { echo "$value;"; }
    	echo "\n";
      }
      
      /*
    	while (OCIFetchInto($iStatement, &$results, OCI_ASSOC+OCI_RETURN_NULLS))
    	{
          // returns ';' delimited string containing all keys and all values
          echo array_reduce(array_keys($results), "returnArray") . "\n";
    	  echo array_reduce($results, "returnArray") . "\n";
    	}
      */
    }
    
    // create a ';' delimited string containing all elements of the array
    function returnArray($val0, $val1) { return $val0 . ";" . $val1; }
    
    ?>
    

HTML Test for Web Proxy

The following html code can be used to test the php proxy listed above.

    <HTML>
    <BODY>
    <FORM method=post action="DatabaseProxy.php">
    
    QUERY:
    <INPUT ID=sql NAME=sql TYPE=TEXT SIZE=50 VALUE="select sysdate from dual;select again">
    <br>
    USER:
    <INPUT ID=user NAME=user TYPE=TEXT SIZE=25 VALUE=''>
    <BR>
    PASS:
    <INPUT ID=passwd NAME=passwd TYPE=PASSWORD SIZE=25 VALUE=''>
    <INPUT TYPE=SUBMIT VALUE=SUBMIT>
    </FORM>
    </BODY>
    </HTML>