gentoo-overlay/sci-biology/amos/files/amos-3.1.0-fix-build-system.patch

* Use proper AR and not just 'ar'
* Fix build system to build in parallel

--- a/configure.ac
+++ b/configure.ac
@@ -34,6 +34,7 @@
 AC_PROG_INSTALL
 AC_PROG_LN_S
 AC_PROG_RANLIB
+AM_PROG_AR
 AC_PROG_CPP
 AC_PATH_PROG(PERL, [perl], [:])
 AC_PATH_PROG(PYTHON, [python], [:])
--- a/src/Align/Makefile.am
+++ b/src/Align/Makefile.am
@@ -133,7 +133,7 @@
 
 ##-- hash-overlap
 hash_overlap_LDADD = \
-	$(top_builddir)/src/Align/libAlign.a \
+	libAlign.a \
 	$(top_builddir)/src/CelMsg/libCelMsg.a \
 	$(top_builddir)/src/Slice/libSlice.a \
 	$(top_builddir)/src/Common/libCommon.a \
@@ -172,7 +172,7 @@
 
 ##-- make-consensus
 make_consensus_LDADD = \
-	$(top_builddir)/src/Align/libAlign.a \
+	libAlign.a \
 	$(top_builddir)/src/CelMsg/libCelMsg.a \
 	$(top_builddir)/src/Slice/libSlice.a \
 	$(top_builddir)/src/Common/libCommon.a \
@@ -182,7 +182,7 @@
 
 ##-- make-consensus_poly
 make_consensus_poly_LDADD = \
-	$(top_builddir)/src/Align/libAlign_poly.a \
+	libAlign_poly.a \
 	$(top_builddir)/src/CelMsg/libCelMsg.a \
 	$(top_builddir)/src/Slice/libSlice.a \
 	$(top_builddir)/src/Common/libCommon.a \
@@ -192,7 +192,7 @@
 
 ##-- maligntest
 maligntest_LDADD = \
-	$(top_builddir)/src/Align/libAlign.a \
+	libAlign.a \
 	$(top_builddir)/src/CelMsg/libCelMsg.a \
 	$(top_builddir)/src/Slice/libSlice.a \
 	$(top_builddir)/src/Common/libCommon.a \
@@ -202,7 +202,7 @@
 
 ##-- merge-contigs
 merge_contigs_LDADD = \
-	$(top_builddir)/src/Align/libAlign.a \
+	libAlign.a \
 	$(top_builddir)/src/CelMsg/libCelMsg.a \
 	$(top_builddir)/src/Slice/libSlice.a \
 	$(top_builddir)/src/Common/libCommon.a \
@@ -235,7 +235,7 @@
 
 ##-- show-ma-asm
 show_ma_asm_LDADD = \
-	$(top_builddir)/src/Align/libAlign.a \
+	libAlign.a \
 	$(top_builddir)/src/Common/libCommon.a \
 	$(top_builddir)/src/AMOS/libAMOS.a
 show_ma_asm_SOURCES = \
@@ -261,7 +261,7 @@
 
 ##-- simple-overlap
 simple_overlap_LDADD = \
-	$(top_builddir)/src/Align/libAlign.a \
+	libAlign.a \
 	$(top_builddir)/src/CelMsg/libCelMsg.a \
 	$(top_builddir)/src/Slice/libSlice.a \
 	$(top_builddir)/src/Common/libCommon.a \
@@ -272,7 +272,7 @@
 
 ##-- test-align
 test_align_LDADD = \
-	$(top_builddir)/src/Align/libAlign.a \
+	libAlign.a \
 	$(top_builddir)/src/CelMsg/libCelMsg.a \
 	$(top_builddir)/src/Slice/libSlice.a \
 	$(top_builddir)/src/Common/libCommon.a \
--- a/src/Bambus/Bundler/Makefile.am
+++ b/src/Bambus/Bundler/Makefile.am
@@ -47,7 +47,7 @@
 	clk.cc
 
 MarkRepeats_LDADD = \
-	$(top_builddir)/src/Bambus/Bundler/libBundler.a \
+	libBundler.a \
 	$(top_builddir)/src/Common/libCommon.a \
 	$(top_builddir)/src/AMOS/libAMOS.a \
 	$(top_builddir)/src/GNU/libGNU.a
@@ -55,7 +55,7 @@
 	MarkRepeats.cc
 
 OrientContigs_LDADD = \
-	$(top_builddir)/src/Bambus/Bundler/libBundler.a \
+	libBundler.a \
 	$(top_builddir)/src/Common/libCommon.a \
 	$(top_builddir)/src/AMOS/libAMOS.a \
 	$(top_builddir)/src/GNU/libGNU.a
@@ -63,7 +63,7 @@
 	OrientContigs.cc
 
 FilterEdgesByCluster_LDADD = \
-	$(top_builddir)/src/Bambus/Bundler/libBundler.a \
+	libBundler.a \
 	$(top_builddir)/src/Common/libCommon.a \
 	$(top_builddir)/src/AMOS/libAMOS.a \
 	$(top_builddir)/src/GNU/libGNU.a