From 0f6e354b52701e73f567fbe5d604a93e9af355ba Mon Sep 17 00:00:00 2001
From: Olivier Sallou <osallou@debian.org>
Date: Tue, 10 May 2011 07:36:20 +0000
Subject: [PATCH] add legacy package for blast cmd line compatibility

---
 debian/control                        | 10 ++++++++++
 debian/ncbi-blast+-legacy.dirs        |  1 +
 debian/ncbi-blast+-legacy.links       |  8 ++++++++
 debian/patches/lecagy_rename_rpsblast | 11 +++++++++++
 debian/patches/series                 |  1 +
 debian/rules                          |  1 +
 6 files changed, 32 insertions(+)
 create mode 100644 debian/ncbi-blast+-legacy.dirs
 create mode 100644 debian/ncbi-blast+-legacy.links
 create mode 100644 debian/patches/lecagy_rename_rpsblast

diff --git a/debian/control b/debian/control
index 8bf590d6..5c7cb631 100644
--- a/debian/control
+++ b/debian/control
@@ -27,3 +27,13 @@ Description: The next generation suite of BLAST sequence search tools
  database of PSSM’s.
  The NCBI supports a BLAST web page at blast.ncbi.nlm.nih.gov as well as
  a network service.
+
+Package: ncbi-blast+-legacy
+Architecture: all
+Depends: ncbi-blast+
+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.pl script in ncbi-blast+ package.
+ To use those scripts, /var/lib/ncbi-blast+/bin must be added
+ to the PATH.
diff --git a/debian/ncbi-blast+-legacy.dirs b/debian/ncbi-blast+-legacy.dirs
new file mode 100644
index 00000000..c70c9418
--- /dev/null
+++ b/debian/ncbi-blast+-legacy.dirs
@@ -0,0 +1 @@
+/var/lib/ncbi-blast+/bin
diff --git a/debian/ncbi-blast+-legacy.links b/debian/ncbi-blast+-legacy.links
new file mode 100644
index 00000000..1c024bdd
--- /dev/null
+++ b/debian/ncbi-blast+-legacy.links
@@ -0,0 +1,8 @@
+var/lib/ncbi-blast+/bin/legacy.sh var/lib/ncbi-blast+/bin/blastall
+var/lib/ncbi-blast+/bin/legacy.sh var/lib/ncbi-blast+/bin/megablast
+var/lib/ncbi-blast+/bin/legacy.sh var/lib/ncbi-blast+/bin/blastpgp
+var/lib/ncbi-blast+/bin/legacy.sh var/lib/ncbi-blast+/bin/bl2seq
+var/lib/ncbi-blast+/bin/legacy.sh var/lib/ncbi-blast+/bin/rpsblast
+var/lib/ncbi-blast+/bin/legacy.sh var/lib/ncbi-blast+/bin/fastacmd
+var/lib/ncbi-blast+/bin/legacy.sh var/lib/ncbi-blast+/bin/formatdb
+var/lib/ncbi-blast+/bin/legacy.sh var/lib/ncbi-blast+/bin/seedtop
diff --git a/debian/patches/lecagy_rename_rpsblast b/debian/patches/lecagy_rename_rpsblast
new file mode 100644
index 00000000..c2ff0664
--- /dev/null
+++ b/debian/patches/lecagy_rename_rpsblast
@@ -0,0 +1,11 @@
+--- a/c++/src/app/blast/legacy_blast.pl
++++ b/c++/src/app/blast/legacy_blast.pl
+@@ -1064,7 +1064,7 @@
+     if (defined $opt_p and $opt_p =~ /f/i) {
+         $retval .= "/rpstblastn";
+     } else {
+-        $retval .= "/rpsblast";
++        $retval .= "/rpsblast+";
+     }
+     $retval .= &add_exe_extension();
+ 
diff --git a/debian/patches/series b/debian/patches/series
index 1992cc9b..d9fc96d2 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1,3 @@
+lecagy_rename_rpsblast
 fix_checks
 fix_gcc46_include_error
diff --git a/debian/rules b/debian/rules
index 2abe6be5..07579d9b 100755
--- a/debian/rules
+++ b/debian/rules
@@ -21,6 +21,7 @@ override_dh_auto_configure:
 override_dh_install:
 	#TODO - can I just use -X.a -Xinclude instead of removing unneeded files later?
 	dh_install
+	cp debian/legacy/legacy.sh debian/ncbi-blast+-legacy/var/lib/ncbi-blast+/bin
 	rm -f ${CURDIR}/debian/ncbi-blast+/usr/bin/*test*
 	#mkdir -p ${CURDIR}/debian/ncbi-blast+-dev/usr/lib/ncbi-blast+
 	rm -f ${CURDIR}/debian/ncbi-blast+/usr/lib/ncbi-blast+/*.a
-- 
2.30.2