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Go through the standard ctakes installation for the distribution you just created: See https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.1+User+Install+Guide. For the rest of this document, we assume ctakes is installed in CTAKES_HOME

1.5) Patch YTEX Distro

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(YTEX 3.2.0 only)

Not needed for YTEX 3.2.1.  Some Some of the install scripts need to be patched (fixed in trunk). Download and unzip  ytex-patch-3.2.0.zip 'over' your installation.  

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cd CTAKES_HOME/bin
chmod ug+x ant ctakes.profile *.sh

2) Unzip YTEX Libraries

Download and unzip ctakes-ytex-lib-3.1.2-SNAPSHOT.zip 'over' your installation. This contains non-APACHE 2.0 license compliant libraries:

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In this file, you specify the database connection parameters. You will find templates in CTAKES_HOME\lib\ctakes-ytex-res-3.2.0[version].jar, under org\apache\ctakes\ytex\ytex.properties.<db type>.example. If you have UMLS installed on your database, specify the umls.schema and umls.catalog properties (see the properties file for an explanation of what these are).

cd %CTAKES_HOME%\resources
mkdir org\apache\ctakes\ytex
@REM extract the mysql example.  change mysql to mssql (for MS SQL Server) or orcl (for Oracle)
jar xf ..\lib\ctakes-ytex-res-*.jar org/apache/ctakes/ytex/ytex.properties.mysql.example
copy org\apache\ctakes\ytex\ytex.properties.mysql.example org\apache\ctakes\ytex\ytex.properties
@REM edit the properties file
notepad org\apache\ctakes\ytex\ytex.properties

cd $CTAKES_HOME/resources
mkdir -p org/apache/ctakes/ytex
# extract the mysql example.  change mysql to mssql (for MS SQL Server) or orcl (for Oracle)
jar xf ../lib/ctakes-ytex-res-*.jar org/apache/ctakes/ytex/ytex.properties.mysql.example
cp org/apache/ctakes/ytex/ytex.properties.mysql.example org/apache/ctakes/ytex/ytex.properties
# edit the properties file
vi org\apache\ctakes\ytex\ytex.properties

6) Install the UMLS in your database (Optional)

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cd /d c:\java\apache-ctakes-3.2.0%CTAKES_HOME%\bin\ctakes-ytex\scripts
..\..\ant.bat -f build-setup.xml -Dlog4j.conf=CTAKES_HOME\config\log4j.xml all > setup.out 2>&1

linux: From a shell, cd to the CTAKES_HOME directory, set the environment, make sure necessary scripts are executable, and execute the ant script:

chmod u+x ${HOME}/ctakes.profile
. ${HOME}/ctakes.profile
cd ${CTAKES_HOME}/bin
chmod u+x ant
chmod u+x *.sh
cd ctakes-ytex/scripts
nohup ../../ant -f build-setup.xml -Dlog4j.conf=CTAKES_HOME/config/log4j.xml all > setup.out 2>&1 &
tail -f setup.out

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