added uchime_src folder. added biom parameter to make.shared. added biom as a current...

[mothur.git] / uchime_src / mk

diff --git a/uchime_src/mk b/uchime_src/mk
new file mode 100755 (executable)
index 0000000..24aeba0
--- /dev/null
+++ b/uchime_src/mk
@@ -0,0 +1,27 @@
+#!/bin/bash
+CPPNames='addtargets2 alignchime alignchimel alnparams alpha alpha2 fractid getparents globalalign2 make3way mx myutils path searchchime seqdb setnucmx sfasta tracebackbit uchime_main usort viterbifast writechhit'
+ObjNames='addtargets2.o alignchime.o alignchimel.o alnparams.o alpha.o alpha2.o fractid.o getparents.o globalalign2.o make3way.o mx.o myutils.o path.o searchchime.o seqdb.o setnucmx.o sfasta.o tracebackbit.o uchime_main.o usort.o viterbifast.o writechhit.o'
+
+rm -f *.o mk.stdout mk.stderr tmp.stderr
+
+for CPPName in $CPPNames
+do
+  echo $CPPName >> /dev/tty
+  g++ $ENV_GCC_OPTS -c -O3 -msse2 -mfpmath=sse -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 $CPPName.cpp -o $CPPName.o  >> mk.stdout 2>> tmp.stderr
+       cat tmp.stderr
+       cat tmp.stderr >> mk.stderr
+       rm -f tmp.stderr
+done
+
+LINK_OPTS= 
+if [ `uname -s` == Linux ] ; then
+    LINK_OPTS=-static
+fi
+g++ $LINK_OPTS $ENV_LINK_OPTS -g -o uchime $ObjNames >> mk.stdout 2>> tmp.stderr
+cat tmp.stderr
+cat tmp.stderr >> mk.stderr
+rm -f tmp.stderr
+
+strip uchime
+ls -lh uchime
+sum uchime