debian/bbmap-jni.install

+jni/*.so	usr/lib/jni

debian/bbmap.install

+*.jar		usr/share/java

debian/control

@@ -16,7 +16,7 @@ Package: bbmap
 Architecture: all
 Depends: ${java:Depends},
          ${misc:Depends}
-Description: short read aligner, and other bioinformatic tools.
+Description: short read aligner and other bioinformatic tools
  BBMap: Short read aligner for DNA and RNA-seq data. Capable of handling
  arbitrarily large genomes with millions of scaffolds. Handles Illumina,
  PacBio, 454, and other reads; very high sensitivity and tolerant of
@@ -35,3 +35,16 @@ Description: short read aligner, and other bioinformatic tools.
  .
  BBDuk: Filters, trims, or masks reads with kmer matches to an
  artifact/contaminant file.
+
+Package: bbmap-jni
+Architecture: any
+Depends: ${shlibs:Depends},
+         ${misc:Depends}
+Description: short read aligner and other bioinformatic tools - JNI library
+ BBMap: Short read aligner for DNA and RNA-seq data. Capable of handling
+ arbitrarily large genomes with millions of scaffolds. Handles Illumina,
+ PacBio, 454, and other reads; very high sensitivity and tolerant of
+ errors and numerous large indels.
+ .
+ This package contains the architecture dependant library for the bbmap
+ tools.

debian/copyright

@@ -2,6 +2,7 @@ Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: BBmap
 Source: https://sourceforge.net/projects/bbmap/
 Files-Excluded: *.class
+                *.so
 
 Files: *
 Copyright: 2008-2015 Brian Bushnell, Jon Rood

debian/install

-*.jar	usr/share/java

debian/rules

@@ -19,8 +19,10 @@ override_dh_auto_clean:
 override_dh_clean:
 	dh_clean
 	find . -name "*.class" -delete
+	find . -name "*.so" -delete
 
 override_dh_auto_build:
+	cd jni && make -f makefile.linux
 	jh_build $(DEB_SOURCE).jar current
 
 override_dh_install:
@@ -35,3 +37,7 @@ override_dh_install:
 		    $${scr} > $(PKGBINDIR)/`basename $${scr} .sh` ; \
 	    fi ; \
 	done
+
+override_dh_fixperms:
+	dh_fixperms
+	chmod -x $(PKGBINDIR)/*