Turn blast2 into a transitional package for ncbi-blast+-legacy.

debian/{blast2.*,control,ncbi-tools-bin.*,rules}, make/makedemo.unx:
Turn blast2 into an architecture-independent transitional package for
ncbi-blast+-legacy; move blastcl3 (the only remaining executable) and
associated documentation to ncbi-tools-bin.

NB: ncbi-blast+-legacy just populates /usr/share/ncbi-blast+-bin, so
blast2 contains symlinks from /usr/bin into that directory.  Future
changes to ncbi-blast+-legacy should render this arrangement
unnecessary.

12 files changed, 33 insertions, 85 deletions

diff --git a/debian/blast2.doc-base b/debian/blast2.doc-base
deleted file mode 100644
index 2ac3ab8d..00000000
--- a/debian/blast2.doc-base
+++ /dev/null
@@ -1,14 +0,0 @@
-Document: blast2
-Title: Basic Local Alignment Search Tool
-Author: The National Center for Biotechnology Information
-Abstract: The Basic Local Alignment Search Tool (BLAST) finds regions of
- local similarity between sequences.  The program compares nucleotide or
- protein sequences to sequence databases and calculates the statistical
- significance of matches.  BLAST can be used to infer functional and
- evolutionary relationships between sequences as well as help identify
- members of gene families.
-Section: Science/Biology
-
-Format: HTML
-Index: /usr/share/doc/blast2/index.html
-Files: /usr/share/doc/blast2/*.html
diff --git a/debian/blast2.docs b/debian/blast2.docs
deleted file mode 100644
index d41787f8..00000000
--- a/debian/blast2.docs
+++ /dev/null
@@ -1,2 +0,0 @@
-doc/blast/*.html
-doc/blast/*.pdf
diff --git a/debian/blast2.examples b/debian/blast2.examples
deleted file mode 100644
index ae4cc864..00000000
--- a/debian/blast2.examples
+++ /dev/null
@@ -1 +0,0 @@
-doc/blast/*.pl
diff --git a/debian/blast2.install b/debian/blast2.install
deleted file mode 100644
index 6b487951..00000000
--- a/debian/blast2.install
+++ /dev/null
@@ -1,17 +0,0 @@
-usr/bin/bl2seq
-usr/bin/blast2
-usr/bin/blastall
-usr/bin/blastall_old
-usr/bin/blastcl3
-usr/bin/blastclust
-usr/bin/blastpgp
-usr/bin/copymat
-usr/bin/fastacmd
-usr/bin/formatdb
-usr/bin/formatrpsdb
-usr/bin/impala
-usr/bin/makemat
-usr/bin/megablast
-usr/bin/rpsblast
-usr/bin/seedtop
-usr/bin/taxblast
diff --git a/debian/blast2.links b/debian/blast2.links
new file mode 100644
index 00000000..2750a37d
--- /dev/null
+++ b/debian/blast2.links
@@ -0,0 +1,8 @@
+usr/share/ncbi-blast+/bin/bl2seq    usr/bin/bl2seq
+usr/share/ncbi-blast+/bin/blastall  usr/bin/blastall
+usr/share/ncbi-blast+/bin/blastpgp  usr/bin/blastpgp
+usr/share/ncbi-blast+/bin/fastacmd  usr/bin/fastacmd
+usr/share/ncbi-blast+/bin/formatdb  usr/bin/formatdb
+usr/share/ncbi-blast+/bin/megablast usr/bin/megablast
+usr/share/ncbi-blast+/bin/rpsblast  usr/bin/rpsblast
+usr/share/ncbi-blast+/bin/seedtop   usr/bin/seedtop
diff --git a/debian/blast2.lintian-overrides b/debian/blast2.lintian-overrides
deleted file mode 100644
index 02ddcada..00000000
--- a/debian/blast2.lintian-overrides
+++ /dev/null
@@ -1 +0,0 @@
-blast2: menu-icon-missing usr/share/pixmaps/ncbilogo.xpm
diff --git a/debian/changelog b/debian/changelog
index 414e53d1..5218e187 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -12,6 +12,10 @@ ncbi-tools6 (6.1.20160908-1) UNRELEASED; urgency=medium
 
   [ Aaron M. Ucko ]
   * Reinstate direct upstream changes lost in merge.
+  * debian/{blast2.*,control,ncbi-tools-bin.*,rules}, make/makedemo.unx:
+    Turn blast2 into an architecture-independent transitional package for
+    ncbi-blast+-legacy; move blastcl3 (the only remaining executable) and
+    associated documentation to ncbi-tools-bin.
   * debian/libncbi6(-dev).install, make/makeshlib.unx: Account for new
     libconnssl library.
 
diff --git a/debian/control b/debian/control
index 08028232..2ae79433 100644
--- a/debian/control
+++ b/debian/control
@@ -57,7 +57,7 @@ Multi-Arch: foreign
 Section: science
 Depends: ncbi-data,
          ${misc:Depends}
-Recommends: blast2
+Recommends: ncbi-blast+
 Replaces: ncbi-data (= 6.1.20081116a-1)
 Description: large rRNA BLAST databases distributed with the NCBI toolkit
  This package contains some ribosomal RNA BLAST databases distributed
@@ -75,17 +75,20 @@ Depends: libncbi6 (<< ${source:Upstream-Version}.1),
          libncbi6 (>= ${source:Upstream-Version}),
          ${misc:Depends},
          ${shlibs:Depends}
-Suggests: blast2,
-          libvibrant6b,
+Suggests: libvibrant6b,
+          ncbi-blast+,
           ncbi-tools-x11
-Breaks: libncbi6-dev (<< 6.1.20110713-3~)
-Replaces: libncbi6-dev (<< 6.1.20110713-3~)
+Breaks: blast2 (<< 2.2.26.20160908),
+        libncbi6-dev (<< 6.1.20110713-3~)
+Replaces: blast2 (<< 2.2.26.20160908),
+          libncbi6-dev (<< 6.1.20110713-3~)
 Description: NCBI libraries for biology applications (text-based utilities)
  This package includes various utilities distributed with the NCBI C SDK,
  including the development tools asntool and errhdr (formerly of
  libncbi6-dev).  None of the programs in this package require X; you can
  find the X-based utilities in the ncbi-tools-x11 package.  BLAST and
- related tools are in a separate package (blast2).
+ related tools now come from a separate source base, corresponding to the
+ ncbi-blast+ and ncbi-blast+-legacy packages.
 
 Package: ncbi-tools-x11
 Architecture: any
@@ -97,8 +100,7 @@ Depends: libncbi6 (<< ${source:Upstream-Version}.1),
          libvibrant6b (>= ${source:Upstream-Version}),
          ${misc:Depends},
          ${shlibs:Depends}
-Suggests: blast2,
-          ncbi-tools-bin
+Suggests: ncbi-tools-bin
 Description: NCBI libraries for biology applications (X-based utilities)
  This package includes some X-based utilities distributed with the
  NCBI C SDK: Cn3D, Network Entrez, Sequin, ddv, and udv.  These
@@ -106,26 +108,19 @@ Description: NCBI libraries for biology applications (X-based utilities)
  several additional library packages.
 
 Package: blast2
-Architecture: any
+Architecture: all
 Multi-Arch: foreign
 Section: science
-Depends: libncbi6 (<< ${source:Upstream-Version}.1),
-         libncbi6 (>= ${source:Upstream-Version}),
-         ${misc:Depends},
-         ${shlibs:Depends}
+Depends: ncbi-blast+-legacy,
+         ${misc:Depends}
 Suggests: libvibrant6b,
           ncbi-rrna-data,
           ncbi-tools-bin,
           ncbi-tools-x11
 Conflicts: ncbi-blast
-Description: Basic Local Alignment Search Tool
- The famous sequence alignment program. This is "official" NCBI version,
- #2. The blastall executable allows you to give a nucleotide or protein
- sequence to the program. It is compared against databases and a summary of
- matches is returned to the user.
- .
- Note that databases are not included in Debian; they must be retrieved
- manually.
+Description: transitional package to ncbi-blast+-legacy
+ This is a temporary transitional package, and will be safe to remove once
+ ncbi-blast+-legacy starts populating /usr/bin itself.
 Homepage: http://www.ncbi.nih.gov/BLAST/
 
 Package: libvibrant6b
diff --git a/debian/ncbi-tools-bin.docs b/debian/ncbi-tools-bin.docs
index 3dd06c1e..26ed2568 100644
--- a/debian/ncbi-tools-bin.docs
+++ b/debian/ncbi-tools-bin.docs
@@ -1,3 +1,4 @@
 doc/README.asn2xml
+doc/blast
 doc/gene2xml.txt
 doc/tbl2asn.txt
diff --git a/debian/ncbi-tools-bin.install b/debian/ncbi-tools-bin.install
index b3834ac5..cc93e116 100644
--- a/debian/ncbi-tools-bin.install
+++ b/debian/ncbi-tools-bin.install
@@ -10,6 +10,7 @@ usr/bin/asndisc
 usr/bin/asnmacro
 usr/bin/asntool
 usr/bin/asnval
+usr/bin/blastcl3
 usr/bin/checksub
 usr/bin/cleanasn
 usr/bin/debruijn
diff --git a/debian/rules b/debian/rules
index 457eb1e7..a6bf1244 100755
--- a/debian/rules
+++ b/debian/rules
@@ -63,11 +63,7 @@ else
 export LD_LIBRARY_PATH:=$(CURDIR)/shlib:$(LD_LIBRARY_PATH)
 endif
 
-# Apps which should be multithreaded if possible.
-MTAPPS = blast blastall blastall_old blastpgp seedtop megablast rpsblast \
-         blastclust
-
-VIB = Psequin sbtedit udv ddv blastcl3 taxblast idfetch bl2seq asn2gb tbl2asn \
+VIB = Psequin sbtedit udv ddv blastcl3 taxblast idfetch asn2gb tbl2asn \
       gene2xml entrez2 gbseqget asn2all asn2asn asn2fsa asn2xml asndisc \
       asnmacro asnval cleanasn insdseqget nps2gps spidey trna2sap trna2tbl \
       $(OGL_TARGETS)
@@ -114,10 +110,6 @@ override_dh_auto_build-arch:
 # users who want the Vibrant UI can use vibrate(1).
 	$(MAKE_IN_BUILD) -f makedemo.unx $(COMMON_FLAGS) $(USESHLIB) \
 	    CFLAGS1="-c $(CFLAGS)" VIBLIBS= VIBFLAG= LIB50=-lpcre
-	-cd build && rm -f $(MTAPPS)
-	$(MAKE_IN_BUILD) -f makedemo.unx $(COMMON_FLAGS) $(USESHLIB) \
-	    CFLAGS1="-c $(CFLAGS)" VIBLIBS= VIBFLAG= THREAD_OBJ="$(THREAD_OBJ)" \
-	    THREAD_OTHERLIBS="$(MT_OTHERLIBS)" $(MTAPPS)
 # Don't bother passing OGLLIBS or VIBLIBS, which apps don't use directly.
 	$(MAKE_IN_BUILD) -f makenet.unx $(COMMON_FLAGS) $(USESHLIB) \
 	    CFLAGS1="-c $(CFLAGS)" THREAD_OBJ="$(THREAD_OBJ)" \
@@ -179,11 +171,8 @@ override_dh_auto_install-arch:
 	rm -f debian/tmp/usr/bin/cdscan
 	rm -f debian/tmp/usr/bin/entrcmd
 #	install -d debian/tmp/usr/lib/cgi-bin
-#	mv debian/tmp/usr/bin/blast.REAL debian/tmp/usr/lib/cgi-bin
-	rm -f debian/tmp/usr/bin/blast.REAL
 	mv debian/tmp/usr/bin/Cn3D debian/tmp/usr/bin/Cn3D-3.0
 #	mv debian/tmp/usr/bin/fmerge debian/tmp/usr/bin/fastamerge
-	mv debian/tmp/usr/bin/blast debian/tmp/usr/bin/blast2
 
 override_dh_auto_install-indep:
 	convert link/mswin/asntool.ico debian/asntool.xpm
@@ -214,7 +203,6 @@ override_dh_installmenu-arch:
 	chmod +x debian/makemenu
 	debian/makemenu debian/ncbi-tools-x11.install
 	debian/makemenu -v debian/ncbi-tools-bin.install
-	debian/makemenu -v debian/blast2.install
 	dh_installmenu
 
 override_dh_installdocs-arch:
@@ -231,9 +219,7 @@ override_dh_installdocs-arch:
 override_dh_installman:
 	dh_link # otherwise runs too late to influence debian/installman
 	chmod +x debian/installman
-ifneq "" "$(filter blast2, $(shell dh_listpackages))"
-	debian/installman blast2
-	debian/installman blast2 blast
+ifneq "" "$(filter ncbi-tools-bin, $(shell dh_listpackages))"
 	debian/installman ncbi-tools-bin
 	debian/installman ncbi-tools-x11
 endif
@@ -250,7 +236,7 @@ override_dh_strip-arch:
 	dh_strip -plibvibrant6b --dbg-package=libvibrant6b-dbg
 	dh_strip -Nlibncbi6     -Nlibvibrant6b
 
-override_dh_gencontrol-arch:
+override_dh_gencontrol-indep:
 	dh_gencontrol  -pblast2 -- -v$(BLAST_VERSION_FULL)
 	dh_gencontrol  -Nblast2
 
diff --git a/make/makedemo.unx b/make/makedemo.unx
index 8a670419..84bbc77e 100644
--- a/make/makedemo.unx
+++ b/make/makedemo.unx
@@ -274,12 +274,6 @@ formatrpsdb : formatrpsdb.c
 	$(CC) -o formatrpsdb $(LDFLAGS) formatrpsdb.c $(LIB23) \
 		$(LIB60) $(LIB2) $(LIB1)
 
-# blast (reincarnation of blastall from algo/blast sources)
-
-blast : blast_driver.c
-	$(CC) -o blast $(LDFLAGS) blast_driver.c $(THREAD_OBJ) $(LIB61) \
-		$(LIB60) $(LIB23) $(LIB2) $(LIB1) $(THREAD_OTHERLIBS)
-
 debruijn : debruijn.c
 	$(CC) -o debruijn $(LDFLAGS) debruijn.c $(LIB60) $(LIB1)
 # blastall
@@ -288,12 +282,6 @@ blastall : blastall.c $(THREAD_OBJ)
 	$(CC) -o blastall $(LDFLAGS) blastall.c $(THREAD_OBJ) $(LIB61) \
 		$(LIB60) $(LIB23) $(LIB2) $(LIB1) $(THREAD_OTHERLIBS)
 
-# blastall_old  (version of blastall that does not link in new algo/blast libs).
-
-blastall_old : blastall.c $(THREAD_OBJ)
-	$(CC) -o blastall_old $(LDFLAGS) -DBLASTALL_TOOLS_ONLY blastall.c \
-		$(THREAD_OBJ) $(LIB23) $(LIB2) $(LIB1) $(THREAD_OTHERLIBS)
-
 # blastpgp
 
 blastpgp : blastpgp.c $(THREAD_OBJ)