add legacy package for blast cmd line compatibility

diff --git a/debian/control b/debian/control
index 8bf590d64e47fb3ef36d3dd1227123789e2188a7..5c7cb6314cb24440ff8dc363946fa8116297e33e 100644 (file)
--- 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 (file)
index 0000000..c70c941
--- /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 (file)
index 0000000..1c024bd
--- /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 (file)
index 0000000..c2ff066
--- /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 1992cc9b77d713f5b8c62227a5c50505931915ab..d9fc96d2e72a9a37181234cf64c02076a5e09ac5 100644 (file)
--- 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 2abe6be5a8797e4fd0cd62f4768b02d2ca966d1f..07579d9b954b255660a0b16de81938a6170990a8 100755 (executable)
--- 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