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19 results

writedb_entry

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    “kpepper” authored
    Changed EBI DbFetch code so that the function works again. Added latest picard jar. More work on CRAM file loading. Updated/added scripts for application start. Small tweaks to makefile/ant. Removed gff2embl and gene_builder. Recreated evosuite tests.
    c743a79e
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    writedb_entry 2.16 KiB
    #!/bin/sh -
    #
    # This script reads and writes entries from a database.
    # Examples:
    # writedb_entry -help
    # writedb_entry -s Pf3D7_01 Pf3D7_05 Pf3D7_07
    #
    # The Java JRE to use is taken from the ARTEMIS_JAVA_JRE
    # environment variable. If this is not set then the JRE is defaulted to 
    # a Java 8 version.
    #
    
    #if [ -z "$ARTEMIS_HOME" ]; then
    #  PRG=`readlink -f "$0"`
    #  echo $PRG
    #  ARTEMIS_HOME=`dirname "$PRG"`/..
    #fi
    
    PRG=$0
    
    while [ -h "$PRG" ] ; do
      ls=`ls -ld "$PRG"`
      link=`expr "$ls" : '.*-> \(.*\)$'`
      if expr "$link" : '.*/.*' > /dev/null; then
        PRG="$link"
      else
        PRG="`dirname $PRG`/$link"
      fi
    done
    
    ARTEMIS_HOME=`dirname "$PRG"`/..
    
    # Default Java to use
    if [[ "$ARTEMIS_JAVA_JRE" = "" ]]
    then
    	JAVA=`which java`
    else
    	JAVA_HOME=$ARTEMIS_JAVA_JRE
    	JAVA=$ARTEMIS_JAVA_JRE/bin/java
    fi
    
    JAVA_VERSION=`${JAVA} -version 2>&1`
    echo ${JAVA_VERSION}
    
    CLASSPATH="$ARTEMIS_HOME:$ARTEMIS_HOME/lib/biojava.jar:$ARTEMIS_HOME/lib/jemAlign.jar:$ARTEMIS_HOME/lib/jakarta-regexp-1.2.jar:$ARTEMIS_HOME/lib/postgresql-8.4-701.jdbc3.jar:$CLASSPATH"
    CLASSPATH="$ARTEMIS_HOME/lib/commons-lang-2.6.jar:$CLASSPATH"
    CLASSPATH="$CLASSPATH:$ARTEMIS_HOME/lib/ibatis/ibatis-2.3.4.726.jar:$ARTEMIS_HOME/lib/ibatis/:$ARTEMIS_HOME/lib/ibatis/log4j-1.2.14.jar:$ARTEMIS_HOME/lib/ibatis/cglib-nodep-2.2.jar"
    CLASSPATH="$CLASSPATH:$ARTEMIS_HOME/lib/picard/picard.jar"
    export CLASSPATH
    
    FLAGS="-mx2048m -ms20m -Djdbc.drivers=org.postgresql.Driver -Dibatis"
    DEFAULT_CONNECTION="-Dchado=db.genedb.org:5432/snapshot?genedb_ro -Dread_only"
    
    
    while test $# != 0
        do
        case $1 in
        -Dchado*)
           DEFAULT_CONNECTION="$1" ;;
        -D*)
           FLAGS="$FLAGS $1" ;;
        *) break ;;
        esac
        shift
    done
    
    # searches for the -c option (needs to know the index)
    idx=0
    for arg in "$@"
    do
    	if [ '-c' == "${arg}" ]; then
    		let "nextID = $idx + 1";
    		DEFAULT_CONNECTION="-Dchado=${!nextID}"
    	fi
    	if [ '-l' == "${arg}" ]; then
    		let "nextID = $idx + 2";
                    eval MAPPING_PATH="${!nextID}"
    		CLASSPATH="${MAPPING_PATH}:$CLASSPATH"
    		export CLASSPATH
    	fi
    	let idx++
    done
    
    echo starting to write with flags: $DEFAULT_CONNECTION $FLAGS 1>&2
    
    $JAVA $DEFAULT_CONNECTION $FLAGS uk.ac.sanger.artemis.io.ReadAndWriteEntry "$@"