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--- src/Makefile.in.orig 2016-02-24 03:08:32 UTC
+++ src/Makefile.in
@@ -1207,10 +1207,15 @@ libgc.a: $(libgc_a_OBJECTS) $(libgc_a_DE
-rm -f libgc.a
$(libgc_a_AR) libgc.a $(libgc_a_OBJECTS) $(libgc_a_LIBADD)
$(RANLIB) libgc.a
+
+# $(SAMLIB) and $(SAMPROG) are being mysteriously deleted sometime after they
+# are copied to src. The cp below is a hack to allow the port to build.
libtophat.a: $(libtophat_a_OBJECTS) $(libtophat_a_DEPENDENCIES) $(EXTRA_libtophat_a_DEPENDENCIES)
-rm -f libtophat.a
$(libtophat_a_AR) libtophat.a $(libtophat_a_OBJECTS) $(libtophat_a_LIBADD)
$(RANLIB) libtophat.a
+ cp $(SAMDIR)/$(SAMLIB) $(SAMDIR)/$(SAMPROG) .
+
install-binPROGRAMS: $(bin_PROGRAMS)
@$(NORMAL_INSTALL)
@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
@@ -1281,9 +1286,11 @@ prep_reads$(EXEEXT): $(prep_reads_OBJECT
sam_juncs$(EXEEXT): $(sam_juncs_OBJECTS) $(sam_juncs_DEPENDENCIES) $(EXTRA_sam_juncs_DEPENDENCIES)
@rm -f sam_juncs$(EXEEXT)
$(sam_juncs_LINK) $(sam_juncs_OBJECTS) $(sam_juncs_LDADD) $(LIBS)
+
samtools_0.1.18$(EXEEXT): $(samtools_0_1_18_OBJECTS) $(samtools_0_1_18_DEPENDENCIES) $(EXTRA_samtools_0_1_18_DEPENDENCIES)
- @rm -f samtools_0.1.18$(EXEEXT)
- $(LINK) $(samtools_0_1_18_OBJECTS) $(samtools_0_1_18_LDADD) $(LIBS)
+ #rm -f samtools_0.1.18$(EXEEXT)
+ #$(LINK) $(samtools_0_1_18_OBJECTS) $(samtools_0_1_18_LDADD) $(LIBS)
+
segment_juncs$(EXEEXT): $(segment_juncs_OBJECTS) $(segment_juncs_DEPENDENCIES) $(EXTRA_segment_juncs_DEPENDENCIES)
@rm -f segment_juncs$(EXEEXT)
$(segment_juncs_LINK) $(segment_juncs_OBJECTS) $(segment_juncs_LDADD) $(LIBS)
@@ -1658,7 +1665,7 @@ uninstall-am: uninstall-binPROGRAMS unin
clean-local:
- cd $(SAMDIR) && make clean
+ cd $(SAMDIR) && ${MAKE} clean
tophat2: tophat2.sh
cp tophat2.sh tophat2 && chmod 755 tophat2
@@ -1669,7 +1676,8 @@ tophat: tophat.py
$(SAMPROG): $(SAMLIB)
$(SAMLIB):
- cd $(SAMDIR) && make $(SAMPROG) && cp $(SAMLIB) $(SAMPROG) ..
+ cd $(SAMDIR) && ${MAKE} $(SAMPROG)
+ cp $(SAMDIR)/$(SAMLIB) $(SAMDIR)/$(SAMPROG) .
install-data-hook:
cp -r intervaltree sortedcontainers $(DESTDIR)$(bindir)
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