rename and recode (to keep instep with otterlace) of script to test zmap and otterlace

scripts/test_zmap_otterlace.sh → scripts/zmap_otterlace.sh

 #!/bin/sh
-############################################################
-# Script to test zmap with otterlace
 
-# Change these few variables to point to the correct places
+SCRIPT_NAME=$(basename $0)
+INITIAL_DIR=$(pwd)
+ SCRIPT_DIR=$(dirname $0)
+if ! echo $SCRIPT_DIR | egrep -q "(^)/" ; then
+    BASE_DIR=$INITIAL_DIR/$SCRIPT_DIR
+else
+    BASE_DIR=$SCRIPT_DIR
+fi
 
-# This should be the current live code for otter.
-# Try ls -lt /software/anacode/otter
-RELEASE=otter_rel47_zmap
+. $BASE_DIR/zmap_functions.sh || { echo "Failed to load zmap_functions.sh"; exit 1; }
 
-# Change the location of this to be where your zmap to test is.
-ZMAP_TO_TEST=""
-ZMAP_TO_TEST=/var/tmp/rds/ZMap/src/build/linux
 
-############################################################
-# Nothing much to change below here...
+zmap_message_out "Start of script."
 
-SOFTWARE=/software/anacode
-OTTER_CONFIG=$HOME/.otter_config
-OTTER_HOME=$SOFTWARE/otter/$RELEASE
-export OTTER_HOME
 
-if [ ! -d $OTTER_HOME ]; then
-    echo
-    echo "This executable is not available at the moment."
-    echo "Please try the non-test version."
-    echo
-    exit 1
+# including VARIABLE=VALUE settings from command line
+if [ $# -gt 0 ]; then
+    eval "$*"
 fi
 
-script='otterlace'
+# otter_root is immutable
+otter_root="/software/anacode/otter"
 
-#. $SOFTWARE/bin/setup_anacode_env
+zmap_check ${RELEASE:="otter_production_main"}
+zmap_check ${OTTER_HOME:="$otter_root/$RELEASE"}
+zmap_check ${ZMAP_HOME:="$HOME"}
+zmap_check ${ZMAP_BIN_DIR:="$OTTER_HOME/bin"}
+zmap_check ${TK_OTTER_HOME:=$OTTER_HOME}
+zmap_check ${ACEDB_HOME:="/nfs/disk100/acedb/RELEASE.DEVELOPMENT/bin.LINUX_4"}
+
+export OTTER_HOME ZMAP_HOME
+
+zmap_message_out "Using OTTER_HOME '$OTTER_HOME'"
+zmap_message_out "Using TK_OTTER_HOME '$TK_OTTER_HOME'"
+zmap_message_out "Using ZMAP_HOME '$ZMAP_HOME'"
+zmap_message_out "Using ZMAP_BIN_DIR '$ZMAP_BIN_DIR'"
 
-# This should be in setup_env
-################## START OF SETUP_ENV ######################
-PERL5LIB="\
-$OTTER_HOME/tk:\
-$OTTER_HOME/PerlModules:\
-$OTTER_HOME/ensembl-ace:\
-$OTTER_HOME/ensembl-otter/modules:\
-$OTTER_HOME/ensembl-pipeline/modules:\
-$OTTER_HOME/ensembl/modules:\
-$OTTER_HOME/ensembl_head/modules:\
-$OTTER_HOME/bioperl-0.7.2:\
-$OTTER_HOME/bioperl-1.2.3-patched:\
-$OTTER_HOME/biodas-1.02:\
-$OTTER_HOME/perl"
-export PERL5LIB
 
 otterlib="$OTTER_HOME/lib"
 if [ -n "$LD_LIBRARY_PATH" ]
@@ -57,7 +47,7 @@ else
 fi
 export LD_LIBRARY_PATH
 
-otterbin="$OTTER_HOME/bin"
+otterbin="$ZMAP_BIN_DIR:$OTTER_HOME/bin:/software/anacode/bin:/software/pubseq/bin/EMBOSS-5.0.0/bin"
 if [ -n "$PATH" ]
 then
     PATH="$otterbin:$PATH"
@@ -79,41 +69,22 @@ export WUBLASTMAT
 ACEDB_NO_BANNER=1
 export ACEDB_NO_BANNER
 
-#################### END OF SETUP_ENV #######################
-
-# Now _prepend_ our path to the PATH setup by above.
-
-#emboss_prefix=/nfs/team71/analysis/rds/emboss
-
-if [ "x$emboss_prefix" != "x" ]; then
-    PATH="$emboss_prefix/bin:$PATH"
-    if [ "x$LD_LIBRARY_PATH" == "x" ]; then
-	LD_LIBRARY_PATH="$emboss_prefix/lib"
-    else
-	LD_LIBRARY_PATH="$emboss_prefix/lib:$LD_LIBRARY_PATH"
-    fi
-fi
-
-if [ "x$ZMAP_TO_TEST" != "x" ]; then
-    PATH="$ZMAP_TO_TEST:$PATH"
-fi
+#cp -f "$OTTER_HOME/acedbrc" ~/.acedbrc
 
+PERL5LIB="\
+$TK_OTTER_HOME/ensembl-otter/tk:\
+$OTTER_HOME/PerlModules:\
+$OTTER_HOME/ensembl-ace:\
+$OTTER_HOME/ensembl-otter/modules:\
+$OTTER_HOME/ensembl-pipeline/modules:\
+$OTTER_HOME/ensembl/modules:\
+$OTTER_HOME/ensembl_head/modules:\
+$OTTER_HOME/bioperl-0.7.2:\
+$OTTER_HOME/bioperl-1.2.3-patched:\
+$OTTER_HOME/biodas-1.02:\
+$OTTER_HOME/perl"
 
-enable_zmap()
-{
-    echo "[client]"           >> $OTTER_CONFIG
-    echo "show_zmap=enable"   >> $OTTER_CONFIG
-    echo "zmap_main_window=1" >> $OTTER_CONFIG
-}
+export PERL5LIB
 
-if [ -f $OTTER_CONFIG ]; then
-    # If it already exists
-    SHOW_ZMAP=`grep show_zmap=enable $OTTER_CONFIG`
-    if [ "x$SHOW_ZMAP" == "x" ]; then
-	enable_zmap
-    fi
-else
-	enable_zmap
-fi
+exec /software/bin/perl "$OTTER_HOME/ensembl-otter/tk/otterlace" $@
 
-exec /software/bin/perl -w "$OTTER_HOME/tk/$script" $@