From: Aaron M. Ucko <ucko@debian.org>
Date: Tue, 6 Dec 2016 04:11:56 +0000 (-0500)
Subject: Fully take blast2 over from ncbi-tools6.
X-Git-Tag: archive/raspbian/2.16.0+ds-7+rpi1~1^2~194
X-Git-Url: https://dgit.raspbian.org/?a=commitdiff_plain;h=4d9d362bc3d9ca5c281d28e70f3a2eb119db0c19;p=ncbi-blast%2B.git

Fully take blast2 over from ncbi-tools6.

The C implementation has retired.
---

diff --git a/debian/changelog b/debian/changelog
index 8cf98115..dde2ecdc 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -4,8 +4,9 @@ ncbi-blast+ (2.5.0-2) UNRELEASED; urgency=medium
   * debian/patches/fix_lib_deps: Patch Makefile.blast_macros.mk to add blast
     to BLAST_LIBS to clear up link errors that could otherwise occur.
   * debian/control: B-D on libgnutls28-dev to enable HTTPS support.
+  * Fully take blast2 over from ncbi-tools6, whose implementation has retired.
 
- -- Aaron M. Ucko <ucko@debian.org>  Mon, 05 Dec 2016 23:10:10 -0500
+ -- Aaron M. Ucko <ucko@debian.org>  Mon, 05 Dec 2016 23:11:55 -0500
 
 ncbi-blast+ (2.5.0-1) unstable; urgency=medium
 
diff --git a/debian/control b/debian/control
index f0f8b3f7..d56e2cb4 100644
--- a/debian/control
+++ b/debian/control
@@ -47,10 +47,20 @@ Architecture: all
 Multi-Arch: foreign
 Depends: ncbi-blast+,
          ${misc:Depends}
+Breaks: blast2 (<< 1:2.5.0~)
+Replaces: blast2 (<< 1:2.5.0~)
 Description: NCBI Blast legacy call script
  This package adds some fake scripts to call NCBI+ programs
  with the NCBI blast command line. It makes use of the
  legacy_blast script in ncbi-blast+ package.
- .
- To use those scripts, /usr/share/ncbi-blast+/bin must be added
- to the PATH.
+
+Package: blast2
+Architecture: all
+Multi-Arch: foreign
+Section: oldlibs
+Priority: extra
+Depends: ncbi-blast+-legacy,
+         ${misc:Depends}
+Description: transitional dummy package to ncbi-blast+-legacy
+ This is a transitional dummy package for ncbi-blast+-legacy.
+ It can safely be removed.
diff --git a/debian/ncbi-blast+-legacy.dirs b/debian/ncbi-blast+-legacy.dirs
index da6a4081..415f082d 100644
--- a/debian/ncbi-blast+-legacy.dirs
+++ b/debian/ncbi-blast+-legacy.dirs
@@ -1 +1 @@
-/usr/share/ncbi-blast+/bin
+/usr/bin
diff --git a/debian/ncbi-blast+-legacy.links b/debian/ncbi-blast+-legacy.links
deleted file mode 100644
index c7320566..00000000
--- a/debian/ncbi-blast+-legacy.links
+++ /dev/null
@@ -1,8 +0,0 @@
-usr/share/ncbi-blast+/bin/legacy.sh usr/share/ncbi-blast+/bin/blastall
-usr/share/ncbi-blast+/bin/legacy.sh usr/share/ncbi-blast+/bin/megablast
-usr/share/ncbi-blast+/bin/legacy.sh usr/share/ncbi-blast+/bin/blastpgp
-usr/share/ncbi-blast+/bin/legacy.sh usr/share/ncbi-blast+/bin/bl2seq
-usr/share/ncbi-blast+/bin/legacy.sh usr/share/ncbi-blast+/bin/rpsblast
-usr/share/ncbi-blast+/bin/legacy.sh usr/share/ncbi-blast+/bin/fastacmd
-usr/share/ncbi-blast+/bin/legacy.sh usr/share/ncbi-blast+/bin/formatdb
-usr/share/ncbi-blast+/bin/legacy.sh usr/share/ncbi-blast+/bin/seedtop
diff --git a/debian/rules b/debian/rules
index 88bb1e33..7ba296d1 100755
--- a/debian/rules
+++ b/debian/rules
@@ -43,6 +43,8 @@ export CFLAGS CPPFLAGS CXXFLAGS LDFLAGS MAKE
 DEB_CONFIGURE_EXTRA_FLAGS +=  CFLAGS_FOR_BUILD="$(CFLAGS) -fPIE"
 DEB_CONFIGURE_EXTRA_FLAGS += LDFLAGS_FOR_BUILD="$(LDFLAGS)"
 
+BLAST2_VERSION=1:$(shell dpkg-parsechangelog | awk '/^Version:/ { print $$2 }')
+
 llp=LD_LIBRARY_PATH
 override_dh_auto_configure:
 	cd c++  &&  $(llp)=$(CURDIR)/c++/BUILD/lib$${$(llp)+:$$$(llp)} \
@@ -62,7 +64,7 @@ override_dh_auto_test:
 	-cat c++/BUILD/build/check.sh.out_err
 
 instroot = debian/ncbi-blast+/usr
-leg_bin = debian/ncbi-blast+-legacy/usr/share/ncbi-blast+/bin
+leg_bin = debian/ncbi-blast+-legacy/usr/bin
 override_dh_auto_install-arch:
 	# cp c++/BUILD/lib/*.so $(instroot)/lib/ncbi-blast+/
 	cp c++/BUILD/bin/*    $(instroot)/bin/
@@ -88,7 +90,12 @@ override_dh_install-arch:
 	xargs cp -v -t $(instroot)/lib/ncbi-blast+
 
 override_dh_install-indep:
-	if test -d $(leg_bin); then cp debian/legacy/legacy.sh $(leg_bin)/; fi
+	#if test -d $(leg_bin); then cp debian/legacy/legacy.sh $(leg_bin)/; fi
+	for x in blastall megablast blastpgp bl2seq rpsblast fastacmd formatdb \
+	         seedtop; do \
+	    sed -e "s/.{.*}/$$x/" debian/legacy/legacy.sh > $(leg_bin)/$$x; \
+	    chmod +x $(leg_bin)/$$x; \
+	done
 
 override_dh_clean:
 	cp c++/configure.orig configure.orig.save
@@ -111,5 +118,9 @@ override_dh_clean:
 	rm -rf c++/BUILD
 	mv configure.orig.save c++/configure.orig
 
+override_dh_gencontrol-indep:
+	dh_gencontrol -pblast2 -- -v$(BLAST2_VERSION)
+	dh_gencontrol -Nblast2
+
 %:
 	dh $@ -Dc++ --with autotools_dev