[med-svn] r9813 - in trunk/packages/sift/trunk/debian: . patches

[Laszlo Kajan]

Author: lkajan-guest
Date: 2012-02-27 18:13:37 +0000 (Mon, 27 Feb 2012)
New Revision: 9813

Modified:
   trunk/packages/sift/trunk/debian/patches/fix_perl_interpreter_and_lib_path
   trunk/packages/sift/trunk/debian/rules
Log:
clean target no longer removes files from upstream

Modified: trunk/packages/sift/trunk/debian/patches/fix_perl_interpreter_and_lib_path
===================================================================
--- trunk/packages/sift/trunk/debian/patches/fix_perl_interpreter_and_lib_path	2012-02-27 17:08:47 UTC (rev 9812)
+++ trunk/packages/sift/trunk/debian/patches/fix_perl_interpreter_and_lib_path	2012-02-27 18:13:37 UTC (rev 9813)
@@ -993,7 +993,7 @@
          strcpy (errorfilename, outfilename);
 --- /dev/null
 +++ b/src/Makefile
-@@ -0,0 +1,42 @@
+@@ -0,0 +1,45 @@
 +include-prefix := $(prefix)
 +lib-prefix := $(prefix)
 +
@@ -1013,8 +1013,11 @@
 +bin: $(BIN)
 +
 +clean:
-+	rm -rf *.o $(BIN)
++	rm -f *.o $(BIN)
 +
++distclean: clean
++	rm -f deps.mk
++
 +install:
 +	mkdir -p $(DESTDIR)$(prefix)/lib/sift/bin && \
 +	cp -a \
@@ -1028,7 +1031,7 @@
 +
 +help:
 +
-+.PHONY: all bin clean help install
++.PHONY: all bin clean distclean help install
 +
 +deps.mk:
 +	$(CC) -MM $(CFLAGS) $(addsuffix .c,$(BIN)) > $@

Modified: trunk/packages/sift/trunk/debian/rules
===================================================================
--- trunk/packages/sift/trunk/debian/rules	2012-02-27 17:08:47 UTC (rev 9812)
+++ trunk/packages/sift/trunk/debian/rules	2012-02-27 18:13:37 UTC (rev 9813)
@@ -25,12 +25,8 @@
 	pod2man -c 'User Commands' --release="$(VERSION)" $< > $@
 
 override_dh_auto_clean:
-	rm -rf bin/linux
-	rm -rf bin/solaris
-	( cd bin ; rm -f choose_seqs_via_psiblastseedmedian consensus_to_seq psiblast_res_to_fasta_dbpairwise \
-	clump_output_alignedseq fastaseqs info_on_seqs seqs_from_psiblast_res )
+	if [ -e src/Makefile ]; then make -j$(parallel) -C src prefix=$(prefix) distclean; fi
 	rm -f $(MAN1)
-	if [ -e src/Makefile ]; then make -j$(parallel) -C src prefix=$(prefix) clean; fi
 
 override_dh_auto_build: man
 	make -j$(parallel) -C src prefix=$(prefix) VERSION=$(VERSION) deps.mk && \
@@ -40,7 +36,8 @@
 	make -C src DESTDIR=$(DESTDIR) prefix=$(prefix) install
 
 override_dh_install:
-	dh_install -X.svn -X.swp bin $(prefix)/lib/sift/
+	# lkajan: fastaseqs comes from the blimps package, this source does not have rules for creating it
+	dh_install -X.svn -X.swp -XManuals -Xfastaseqs -Xlinux -Xsolaris bin $(prefix)/lib/sift/
 	dh_install -X.svn -X.swp blimps/docs $(prefix)/share/sift/blimps/
 	#Links are created by debian/links
 	for f in SIFT_for_submitting_fasta_seq.csh SIFT_for_submitting_NCBI_gi_id.csh; do \
@@ -50,7 +47,7 @@
 		sed --in-place -e 's|\b__MAKE_PREFIX__\b|$(prefix)|g;s|__SIFT_SCRIPTDIR__|$(SIFT_SCRIPTDIR)|g;s|__SIFT_BINDIR__|$(SIFT_BINDIR)|g;' $(DESTDIR)$(SIFT_SCRIPTDIR)/$$f; \
 	done;
 	chmod +x $(DESTDIR)$(prefix)/lib/sift/bin/perlscripts/separate_query_from_rest_of_seqs.pl
-	# look out: DNA_PROT_SUBROUTINES.pl is really a module(should be pm)!
+	# look out: DNA_PROT_SUBROUTINES.pl is really a module (should be pm)!
 	for f in IntersectFeatures.jar SIFT_subroutines.pm DNA_PROT_SUBROUTINES.pl; do \
 		chmod -x $(DESTDIR)$(prefix)/lib/sift/bin/$$f; \
 	done;