Drop clustalw from main tools script

Author: bbimber

SequenceAnalysis/pipeline_code/extra_tools_install.sh

@@ -379,3 +379,32 @@ then
 else
     echo "Already installed"
 fi
+
+#
+#clustalw
+#
+
+echo ""
+echo ""
+echo "%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%"
+echo "Installing ClustalW"
+echo ""
+cd $LKSRC_DIR
+
+if [[ ! -e ${LKTOOLS_DIR}/clustalw2 || ! -z $FORCE_REINSTALL ]];
+then
+    rm -Rf clustal*
+    rm -Rf 1.2.4-cmake.tar.gz
+    rm -Rf $LKTOOLS_DIR/clustalw2
+
+    wget $WGET_OPTS https://github.com/GSLBiotech/clustal-omega/archive/refs/tags/1.2.4-cmake.tar.gz
+    tar -xf 1.2.4-cmake.tar.gz
+    cd clustal-omega-1.2.4-cmake
+    ./configure
+    make
+
+    install ./src/clustalw2 $LKTOOLS_DIR/clustalw2
+
+else
+    echo "Already installed"
+fi

SequenceAnalysis/pipeline_code/sequence_tools_install.sh

@@ -999,37 +999,6 @@ else
 fi
 
 
-#
-#clustalw
-#
-
-echo ""
-echo ""
-echo "%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%"
-echo "Installing ClustalW"
-echo ""
-cd $LKSRC_DIR
-
-if [[ ! -e ${LKTOOLS_DIR}/clustalw2 || ! -z $FORCE_REINSTALL ]];
-then
-    rm -Rf clustalw-*
-    rm -Rf $LKTOOLS_DIR/clustalw2
-
-    wget $WGET_OPTS http://www.clustal.org/download/current/clustalw-2.1.tar.gz
-    gunzip clustalw-2.1.tar.gz
-    tar -xf clustalw-2.1.tar
-    gzip clustalw-2.1.tar
-    cd clustalw-2.1
-    ./configure
-    make
-
-    install ./src/clustalw2 $LKTOOLS_DIR/clustalw2
-
-else
-    echo "Already installed"
-fi
-
-
 #
 #muscle
 #