diff --git a/compile.sh b/compile.sh
index 10de8c406..45c10325c 100755
--- a/compile.sh
+++ b/compile.sh
@@ -1,8 +1,8 @@
 #!/bin/bash 
-# this script assumes that all 3rd-party dependencies are installed under ./opt
+# if not supplied otherwise, this script assumes that all 3rd-party dependencies are installed under ./opt
 # you can install all 3rd-party dependencies by running make -f contrib/Makefiles/install-dependencies.gmake
 
 set -e -o pipefail
-opt=$(pwd)/opt
-./bjam --with-irstlm=$opt/irstlm-5.80.08 --with-boost=$opt --with-cmph=$opt --with-xmlrpc-c=$opt --with-mm --with-probing-pt -j$(getconf _NPROCESSORS_ONLN) $@
+OPT=${OPT:-$(pwd)/OPT}
+./bjam --with-irstlm=$OPT/irstlm-5.80.08 --with-boost=$OPT --with-cmph=$OPT --with-xmlrpc-c=$OPT --with-mm --with-probing-pt -j$(getconf _NPROCESSORS_ONLN) $@
 
diff --git a/contrib/Makefiles/install-dependencies.gmake b/contrib/Makefiles/install-dependencies.gmake
index ce29e5172..8262368a8 100644
--- a/contrib/Makefiles/install-dependencies.gmake
+++ b/contrib/Makefiles/install-dependencies.gmake
@@ -56,12 +56,12 @@ sourceforge = http://downloads.sourceforge.net/project
 nproc := $(shell getconf _NPROCESSORS_ONLN)
 sfget  = mkdir -p '${TMP}' && cd '${TMP}' && wget -qO- ${URL} | tar xz 
 configure-make-install  = cd '$1' && ./configure --prefix='${PREFIX}' 
-configure-make-install += && make -j$(getconf _NPROCESSORS_ONLN) && make install
+configure-make-install += && make -j${nproc} && make install
 
 # XMLRPC-C for moses server
 xmlrpc: URL=$(sourceforge)/xmlrpc-c/Xmlrpc-c%20Super%20Stable/1.33.17/xmlrpc-c-1.33.17.tgz
 xmlrpc: TMP=$(CWD)/build/xmlrpc
-xmlrpc: PREFIX=${XMLRPC_PREFIX}
+xmlrpc: override PREFIX=${XMLRPC_PREFIX}
 xmlrpc: | $(call safepath,${XMLRPC_PREFIX}/bin/xmlrpc-c-config)
 $(call safepath,${XMLRPC_PREFIX}/bin/xmlrpc-c-config):
 	$(sfget)
@@ -71,7 +71,7 @@ $(call safepath,${XMLRPC_PREFIX}/bin/xmlrpc-c-config):
 # CMPH for CompactPT
 cmph: URL=$(sourceforge)/cmph/cmph/cmph-2.0.tar.gz
 cmph: TMP=$(CWD)/build/cmph
-cmph: PREFIX=${CMPH_PREFIX}
+cmph: override PREFIX=${CMPH_PREFIX}
 cmph: | $(call safepath,${CMPH_PREFIX}/bin/cmph)
 $(call safepath,${CMPH_PREFIX}/bin/cmph):
 	$(sfget)
@@ -82,20 +82,20 @@ $(call safepath,${CMPH_PREFIX}/bin/cmph):
 irstlm: URL=$(sourceforge)/irstlm/irstlm/irstlm-5.80/irstlm-5.80.08.tgz
 irstlm: TMP=$(CWD)/build/irstlm
 irstlm: VERSION=$(basename $(notdir $(irstlm_url)))
-irstlm: PREFIX=${IRSTLM_PREFIX}
+irstlm: override PREFIX=${IRSTLM_PREFIX}
 irstlm: | $(call safepath,$(IRSTLM_PREFIX)/bin/build-lm.sh)
 $(call safepath,$(IRSTLM_PREFIX)/bin/build-lm.sh):
 	$(sfget)
 	cd $$(find '${TMP}' -name trunk) && ./regenerate-makefiles.sh \
-	&& ./configure --prefix='${PREFIX}' && make -j${shell getconf _NPROCESSORS_ONLN} && make install -j$(shell getconf _NPROCESSORS_ONLN)
+	&& ./configure --prefix='${PREFIX}' && make -j${nproc} && make install -j${nproc}
 	rm -rf ${TMP}
 
 # boost 
 boost: URL=http://sourceforge.net/projects/boost/files/boost/1.59.0/boost_1_59_0.tar.gz/download
 boost: TMP=$(CWD)/build/boost
-boost: PREFIX=${BOOST_PREFIX}
+boost: override PREFIX=${BOOST_PREFIX}
 boost: | $(call safepath,${BOOST_PREFIX}/include/boost)
 $(call safepath,${BOOST_PREFIX}/include/boost):
 	$(sfget)
-	cd '${TMP}/boost_1_59_0' && ./bootstrap.sh && ./b2 --prefix=${PREFIX} -j$(shell getconf _NPROCESSORS_ONLN) install
+	cd '${TMP}/boost_1_59_0' && ./bootstrap.sh && ./b2 --prefix=${PREFIX} -j${nproc} install
 	rm -rf ${TMP}
diff --git a/scripts/ems/example/config.basic b/scripts/ems/example/config.basic
index 006d7022e..257166721 100644
--- a/scripts/ems/example/config.basic
+++ b/scripts/ems/example/config.basic
@@ -51,6 +51,12 @@ ttable-binarizer = "$moses-bin-dir/CreateOnDiskPt 1 1 4 100 2"
 input-tokenizer = "$moses-script-dir/tokenizer/tokenizer.perl -a -l $input-extension"
 output-tokenizer = "$moses-script-dir/tokenizer/tokenizer.perl -a -l $output-extension"
 
+# For Arabic tokenizer try Farasa (download: http://qatsdemo.cloudapp.net/farasa/)
+#  Abdelali, Darwish, Durrani, Mubarak (NAACL demo 2016)
+#  "Farasa: A Fast and Furious Segmenter for Arabic"
+input-tokenizer = "$farasa-dir/farasa_moses.sh"
+
+
 # truecasers - comment out if you do not use the truecaser
 input-truecaser = $moses-script-dir/recaser/truecase.perl
 output-truecaser = $moses-script-dir/recaser/truecase.perl
@@ -389,7 +395,7 @@ alignment-symmetrization-method = grow-diag-final-and
 # 
 #operation-sequence-model = "yes"
 #operation-sequence-model-order = 5
-#operation-sequence-model-settings = "-lmplz '$moses-src-dir/bin/lmplz -S 40% -T $working-dir/model/tmp'"
+#operation-sequence-model-settings = "-lmplz '$moses-src-dir/bin/lmplz -S 40% '"
 #
 # OR if you want to use with SRILM
 #
diff --git a/scripts/ems/example/config.factored b/scripts/ems/example/config.factored
index ef5b81010..6f7beb438 100644
--- a/scripts/ems/example/config.factored
+++ b/scripts/ems/example/config.factored
@@ -51,6 +51,11 @@ ttable-binarizer = "$moses-bin-dir/CreateOnDiskPt 1 1 4 100 2"
 input-tokenizer = "$moses-script-dir/tokenizer/tokenizer.perl -a -l $input-extension"
 output-tokenizer = "$moses-script-dir/tokenizer/tokenizer.perl -a -l $output-extension"
 
+# For Arabic tokenizer try Farasa (download: http://qatsdemo.cloudapp.net/farasa/)
+#  Abdelali, Darwish, Durrani, Mubarak (NAACL demo 2016)
+#  "Farasa: A Fast and Furious Segmenter for Arabic"
+input-tokenizer = "$farasa-dir/farasa_moses.sh"
+
 # truecasers - comment out if you do not use the truecaser
 input-truecaser = $moses-script-dir/recaser/truecase.perl
 output-truecaser = $moses-script-dir/recaser/truecase.perl
diff --git a/scripts/ems/example/config.hierarchical b/scripts/ems/example/config.hierarchical
index 9f389710b..6fb77a18a 100644
--- a/scripts/ems/example/config.hierarchical
+++ b/scripts/ems/example/config.hierarchical
@@ -54,6 +54,11 @@ ttable-binarizer = "$moses-bin-dir/CreateOnDiskPt 1 1 4 100 2"
 input-tokenizer = "$moses-script-dir/tokenizer/tokenizer.perl -a -l $input-extension"
 output-tokenizer = "$moses-script-dir/tokenizer/tokenizer.perl -a -l $output-extension"
 
+# For Arabic tokenizer try Farasa (download: http://qatsdemo.cloudapp.net/farasa/)
+#  Abdelali, Darwish, Durrani, Mubarak (NAACL demo 2016)
+#  "Farasa: A Fast and Furious Segmenter for Arabic"
+input-tokenizer = "$farasa-dir/farasa_moses.sh"
+
 # truecasers - comment out if you do not use the truecaser
 input-truecaser = $moses-script-dir/recaser/truecase.perl
 output-truecaser = $moses-script-dir/recaser/truecase.perl
diff --git a/scripts/ems/example/config.syntax b/scripts/ems/example/config.syntax
index c6133784a..ddde6baad 100644
--- a/scripts/ems/example/config.syntax
+++ b/scripts/ems/example/config.syntax
@@ -54,6 +54,11 @@ ttable-binarizer = "$moses-bin-dir/CreateOnDiskPt 1 1 4 100 2"
 input-tokenizer = "$moses-script-dir/tokenizer/tokenizer.perl -a -l $input-extension"
 output-tokenizer = "$moses-script-dir/tokenizer/tokenizer.perl -a -l $output-extension"
 
+# For Arabic tokenizer try Farasa (download: http://qatsdemo.cloudapp.net/farasa/)
+#  Abdelali, Darwish, Durrani, Mubarak (NAACL demo 2016)
+#  "Farasa: A Fast and Furious Segmenter for Arabic"
+input-tokenizer = "$farasa-dir/farasa_moses.sh"
+
 # truecasers - comment out if you do not use the truecaser
 input-truecaser = $moses-script-dir/recaser/truecase.perl
 output-truecaser = $moses-script-dir/recaser/truecase.perl
diff --git a/scripts/ems/example/config.toy b/scripts/ems/example/config.toy
index 0b2975b22..dff4ed10d 100644
--- a/scripts/ems/example/config.toy
+++ b/scripts/ems/example/config.toy
@@ -51,6 +51,11 @@ ttable-binarizer = "$moses-bin-dir/CreateOnDiskPt 1 1 4 100 2"
 input-tokenizer = "$moses-script-dir/tokenizer/tokenizer.perl -a -l $input-extension"
 output-tokenizer = "$moses-script-dir/tokenizer/tokenizer.perl -a -l $output-extension"
 
+# For Arabic tokenizer try Farasa (download: http://qatsdemo.cloudapp.net/farasa/)
+#  Abdelali, Darwish, Durrani, Mubarak (NAACL demo 2016)
+#  "Farasa: A Fast and Furious Segmenter for Arabic"
+input-tokenizer = "$farasa-dir/farasa_moses.sh"
+
 # truecasers - comment out if you do not use the truecaser
 input-truecaser = $moses-script-dir/recaser/truecase.perl
 output-truecaser = $moses-script-dir/recaser/truecase.perl
diff --git a/scripts/ems/example/config.toy.bilinguallm b/scripts/ems/example/config.toy.bilinguallm
index abda2adc2..f4730a80f 100644
--- a/scripts/ems/example/config.toy.bilinguallm
+++ b/scripts/ems/example/config.toy.bilinguallm
@@ -51,6 +51,11 @@ ttable-binarizer = "$moses-bin-dir/CreateOnDiskPt 1 1 4 100 2"
 input-tokenizer = "$moses-script-dir/tokenizer/tokenizer.perl -a -l $input-extension"
 output-tokenizer = "$moses-script-dir/tokenizer/tokenizer.perl -a -l $output-extension"
 
+# For Arabic tokenizer try Farasa (download: http://qatsdemo.cloudapp.net/farasa/)
+#  Abdelali, Darwish, Durrani, Mubarak (NAACL demo 2016)
+#  "Farasa: A Fast and Furious Segmenter for Arabic"
+input-tokenizer = "$farasa-dir/farasa_moses.sh"
+
 # truecasers - comment out if you do not use the truecaser
 input-truecaser = $moses-script-dir/recaser/truecase.perl
 output-truecaser = $moses-script-dir/recaser/truecase.perl
diff --git a/scripts/generic/moses-parallel.pl b/scripts/generic/moses-parallel.pl
index 7d9d61658..f548bf799 100755
--- a/scripts/generic/moses-parallel.pl
+++ b/scripts/generic/moses-parallel.pl
@@ -59,7 +59,7 @@ my $help=0;
 my $dbg=0;
 my $jobs=4;
 my $cache_model=undef;
-my $mosescmd="$ENV{MOSESBIN}/moses"; #decoder in use
+my $mosescmd="$ENV{MOSESBIN}/moses" if defined $ENV{"MOSESBIN"}; #decoder in use
 my $inputlist=undef;
 my $inputfile=undef;
 my $inputtype=0;
@@ -276,7 +276,7 @@ sub getNbestParameters(){
 #get parameters for search graph computation (possibly from configuration file)
 sub getSearchGraphParameters(){
   if (!$searchgraphlist){
-    open (CFG, "$cfgfile");
+    open (CFG, $cfgfile) or die "Can't read '$cfgfile'";
     while (chomp($_=<CFG>)){
       if (/^\[output-search-graph\]/ || /^\[osg\]/){
 	my $tmp;
@@ -299,7 +299,7 @@ sub getSearchGraphParameters(){
 #get parameters for word graph computation (possibly from configuration file)
 sub getWordGraphParameters(){
   if (!$wordgraphlist){
-    open (CFG, "$cfgfile");
+    open (CFG, $cfgfile) or die "Can't read '$cfgfile'";
     while (chomp($_=<CFG>)){
       if (/^\[output-word-graph\]/ || /^\[owg\]/){
         my $tmp;
@@ -843,12 +843,14 @@ sub concatenate_nbest(){
 
 #computing the length of each input file
     my @in=();
-    open (IN, "${inputfile}.${splitpfx}${idx}.trans");
+    open (IN, "${inputfile}.${splitpfx}${idx}.trans")
+      or die "Failed to open '${inputfile}.${splitpfx}${idx}.trans'";
     @in=<IN>;
     close(IN);
     $inplength{$idx} = scalar(@in);
 
-    open (IN, "${nbestfile}.${splitpfx}${idx}");
+    open (IN, "${nbestfile}.${splitpfx}${idx}")
+      or die "Failed to open '${nbestfile}.${splitpfx}${idx}'";
     while (<IN>){
       my ($code,@extra)=split(/\|\|\|/,$_);
       $code += $offset;
@@ -1078,7 +1080,7 @@ sub safesystem {
 sub getPwdCmd(){
 	my $pwdcmd="pwd";
 	my $a;
-	chomp($a=`which pawd 2> /dev/null | head -1 | awk '{print $1}'`);
+	chomp($a=`which pawd 2> /dev/null | head -1 | awk '{print \$1}'`);
 	if ($a && -e $a){	$pwdcmd=$a;	}
 	return $pwdcmd;
 }
diff --git a/scripts/generic/qsub-wrapper.pl b/scripts/generic/qsub-wrapper.pl
index c282b0600..b419f27fb 100755
--- a/scripts/generic/qsub-wrapper.pl
+++ b/scripts/generic/qsub-wrapper.pl
@@ -252,7 +252,7 @@ sub safesystem {
 sub getPwdCmd(){
 	my $pwdcmd="pwd";
 	my $a;
-	chomp($a=`which pawd 2> /dev/null | head -1 | awk '{print $1}'`);
+	chomp($a=`which pawd 2> /dev/null | head -1 | awk '{print \$1}'`);
 	if ($a && -e $a){	$pwdcmd=$a;	}
 	return $pwdcmd;
 }
diff --git a/scripts/training/clone_moses_model.pl b/scripts/training/clone_moses_model.pl
index 18dc4aa41..488415f8b 100755
--- a/scripts/training/clone_moses_model.pl
+++ b/scripts/training/clone_moses_model.pl
@@ -123,7 +123,7 @@ sub clone_file_or_die {
   my $src = shift;
   my $tgt = shift;
 
-  my $src = resolve($src); # resolve symlinks
+  $src = resolve($src); # resolve symlinks
 
   my $ok = 0;
   if ($symlink) {