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;
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