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227 dpurdie 1 
#! /usr/bin/bash
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########################################################################
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#
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#   JATS Post Installation Setup for SOLARIS/LINUX
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#
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#   This command is to be executed in the directory in which it is found
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#
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#   Note: This MUST be a UNIX format file, not a DOS formatted file
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#
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########################################################################
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#
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#   Determine machine type
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#
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if [ -z "$GBE_MACHTYPE" ] ; then
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	echo "ERROR: GBE_MACHTYPE is not defined"
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	exit 1
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fi
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#
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#   Sanity test
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#
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if [ ! -d ./TOOLS ] ; then
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    echo "ERROR: TOOLS directory not found"
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    exit 1
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fi
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if [ ! -d ./BIN.${GBE_MACHTYPE} ] ; then
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    echo "ERROR: ./BIN.${GBE_MACHTYPE} directory not found"
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    exit 1
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fi
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if [ ! -f ./BIN.${GBE_MACHTYPE}/links.sh ] ; then
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    echo "ERROR: links.sh not found"
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    exit 1
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fi
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#
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#   Ensure some essential scripts are not in DOS format
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#   The TOOLS/*.pl file conversion will ensure that pod2usage() operates
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#
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for file in ./TOOLS/armerge ./BIN.*/links.sh $( find ./TOOLS -name *.pl ); do
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    chmod +w $file
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    dos2unix -ascii $file $file 2>/dev/null
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    chmod -w $file
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done
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#
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#   Make executables executable
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#
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chmod -fR +x ./TOOLS
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chmod -fR +x ./BIN.*
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#
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#   Release links for all targets.
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#
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for dir in ./BIN.*; do
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    if [ -d $dir ] ; then
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        cd $dir
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	echo Processing links in $dir
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        [ -f ./links.sh ] && sh ./links.sh
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        cd -
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    fi
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done
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echo "JATS setup complete"