[med-svn] r6802 - in trunk/packages/ncbi-blast-plus/trunk/debian: . patches

[olivier sallou]

Author: osallou-guest
Date: 2011-05-10 07:36:20 +0000 (Tue, 10 May 2011)
New Revision: 6802

Added:
   trunk/packages/ncbi-blast-plus/trunk/debian/ncbi-blast+-legacy.dirs
   trunk/packages/ncbi-blast-plus/trunk/debian/ncbi-blast+-legacy.links
   trunk/packages/ncbi-blast-plus/trunk/debian/patches/lecagy_rename_rpsblast
Modified:
   trunk/packages/ncbi-blast-plus/trunk/debian/control
   trunk/packages/ncbi-blast-plus/trunk/debian/patches/series
   trunk/packages/ncbi-blast-plus/trunk/debian/rules
Log:
add legacy package for blast cmd line compatibility

Modified: trunk/packages/ncbi-blast-plus/trunk/debian/control
===================================================================
--- trunk/packages/ncbi-blast-plus/trunk/debian/control	2011-05-10 00:36:21 UTC (rev 6801)
+++ trunk/packages/ncbi-blast-plus/trunk/debian/control	2011-05-10 07:36:20 UTC (rev 6802)
@@ -27,3 +27,13 @@
  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.

Added: trunk/packages/ncbi-blast-plus/trunk/debian/ncbi-blast+-legacy.dirs
===================================================================
--- trunk/packages/ncbi-blast-plus/trunk/debian/ncbi-blast+-legacy.dirs	                        (rev 0)
+++ trunk/packages/ncbi-blast-plus/trunk/debian/ncbi-blast+-legacy.dirs	2011-05-10 07:36:20 UTC (rev 6802)
@@ -0,0 +1 @@
+/var/lib/ncbi-blast+/bin

Added: trunk/packages/ncbi-blast-plus/trunk/debian/ncbi-blast+-legacy.links
===================================================================
--- trunk/packages/ncbi-blast-plus/trunk/debian/ncbi-blast+-legacy.links	                        (rev 0)
+++ trunk/packages/ncbi-blast-plus/trunk/debian/ncbi-blast+-legacy.links	2011-05-10 07:36:20 UTC (rev 6802)
@@ -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

Added: trunk/packages/ncbi-blast-plus/trunk/debian/patches/lecagy_rename_rpsblast
===================================================================
--- trunk/packages/ncbi-blast-plus/trunk/debian/patches/lecagy_rename_rpsblast	                        (rev 0)
+++ trunk/packages/ncbi-blast-plus/trunk/debian/patches/lecagy_rename_rpsblast	2011-05-10 07:36:20 UTC (rev 6802)
@@ -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();
+ 

Modified: trunk/packages/ncbi-blast-plus/trunk/debian/patches/series
===================================================================
--- trunk/packages/ncbi-blast-plus/trunk/debian/patches/series	2011-05-10 00:36:21 UTC (rev 6801)
+++ trunk/packages/ncbi-blast-plus/trunk/debian/patches/series	2011-05-10 07:36:20 UTC (rev 6802)
@@ -1,2 +1,3 @@
+lecagy_rename_rpsblast
 fix_checks
 fix_gcc46_include_error

Modified: trunk/packages/ncbi-blast-plus/trunk/debian/rules
===================================================================
--- trunk/packages/ncbi-blast-plus/trunk/debian/rules	2011-05-10 00:36:21 UTC (rev 6801)
+++ trunk/packages/ncbi-blast-plus/trunk/debian/rules	2011-05-10 07:36:20 UTC (rev 6802)
@@ -21,6 +21,7 @@
 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