[med-svn] [Git][med-team/bbmap][master] 9 commits: Delete precompiled jni *.so file

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / bbmap


Commits:
d76deac3 by Andreas Tille at 2018-10-28T05:34:11Z
Delete precompiled jni *.so file

- - - - -
41c2d0b5 by Andreas Tille at 2018-10-28T05:34:41Z
New upstream version 38.26+dfsg
- - - - -
e68cc2e7 by Andreas Tille at 2018-10-28T05:34:49Z
Update upstream source from tag 'upstream/38.26+dfsg'

Update to upstream version '38.26+dfsg'
with Debian dir 787869ed4805220f074157bbea2dbf6a6edd45c1
- - - - -
cbfec077 by Andreas Tille at 2018-10-28T05:37:44Z
Recreate JNI *.so

- - - - -
b234f838 by Andreas Tille at 2018-10-28T05:39:16Z
install JNI

- - - - -
3df97c75 by Andreas Tille at 2018-10-28T05:41:29Z
Fix permissions

- - - - -
e2b14b26 by Andreas Tille at 2018-10-28T05:50:36Z
Fix installation of JNI file

- - - - -
b7a06c51 by Andreas Tille at 2018-10-28T05:51:41Z
Fix synopsis

- - - - -
b092c71e by Andreas Tille at 2018-10-28T07:48:55Z
Separate package for JNI lib

- - - - -


8 changed files:

- + debian/bbmap-jni.install
- + debian/bbmap.install
- debian/manifest → debian/bbmap.manifest
- debian/control
- debian/copyright
- − debian/install
- debian/rules
- − jni/libbbtoolsjni.so


Changes:

=====================================
debian/bbmap-jni.install
=====================================
@@ -0,0 +1 @@
+jni/*.so	usr/lib/jni


=====================================
debian/bbmap.install
=====================================
@@ -0,0 +1 @@
+*.jar		usr/share/java


=====================================
debian/manifest → debian/bbmap.manifest
=====================================


=====================================
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 deleted
=====================================
@@ -1 +0,0 @@
-*.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)/*


=====================================
jni/libbbtoolsjni.so deleted
=====================================
Binary files a/jni/libbbtoolsjni.so and /dev/null differ



View it on GitLab: https://salsa.debian.org/med-team/bbmap/compare/d366ef0443cfc57f90723c13e5df27b463ef9e10...b092c71e542984a7505db404c5f9f21c1c9976af

-- 
View it on GitLab: https://salsa.debian.org/med-team/bbmap/compare/d366ef0443cfc57f90723c13e5df27b463ef9e10...b092c71e542984a7505db404c5f9f21c1c9976af
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