[med-svn] r3603 - trunk/packages/samtools/trunk/debian

Charles Plessy plessy at alioth.debian.org
Fri Jul 10 09:38:28 UTC 2009 

Author: plessy
Date: 2009-07-10 09:38:27 +0000 (Fri, 10 Jul 2009)
New Revision: 3603

Added:
   trunk/packages/samtools/trunk/debian/libbam-dev.install
   trunk/packages/samtools/trunk/debian/reference
   trunk/packages/samtools/trunk/debian/samtools-examples.examples
   trunk/packages/samtools/trunk/debian/samtools.docs
   trunk/packages/samtools/trunk/debian/samtools.install
   trunk/packages/samtools/trunk/debian/samtools.manpages
Removed:
   trunk/packages/samtools/trunk/debian/docs
   trunk/packages/samtools/trunk/debian/install
   trunk/packages/samtools/trunk/debian/manpages
Modified:
   trunk/packages/samtools/trunk/debian/changelog
   trunk/packages/samtools/trunk/debian/control
   trunk/packages/samtools/trunk/debian/copyright
   trunk/packages/samtools/trunk/debian/rules
Log:
Added draft example and library-dev packages.


Modified: trunk/packages/samtools/trunk/debian/changelog
===================================================================
--- trunk/packages/samtools/trunk/debian/changelog	2009-07-09 13:42:46 UTC (rev 3602)
+++ trunk/packages/samtools/trunk/debian/changelog	2009-07-10 09:38:27 UTC (rev 3603)
@@ -1,4 +1,4 @@
-samtools (0.1.3-1) UNRELEASED; urgency=low
+samtools (0.1.5c-1) UNRELEASED; urgency=low
 
   Non-free files found; sort out before upload.
 

Modified: trunk/packages/samtools/trunk/debian/control
===================================================================
--- trunk/packages/samtools/trunk/debian/control	2009-07-09 13:42:46 UTC (rev 3602)
+++ trunk/packages/samtools/trunk/debian/control	2009-07-10 09:38:27 UTC (rev 3603)
@@ -5,7 +5,7 @@
 DM-Upload-Allowed: yes
 Uploaders: Charles Plessy <plessy at debian.org>
 Build-Depends: debhelper (>= 7), cdbs
-Standards-Version: 3.8.0
+Standards-Version: 3.8.2
 Homepage: http://samtools.sourceforge.net
 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/samtools/trunk/?rev=0&sc=0
 Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/samtools/trunk/
@@ -17,4 +17,16 @@
  Samtools is a set of utilities that manipulate alignments in the BAM format.
  It imports from and exports to the SAM (Sequence Alignment/Map) format, does
  sorting, merging and indexing, and allows to retrieve reads in any regions
- swiftly. 
+ swiftly.
+
+Package: libbam-dev
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: libbam
+ ............
+
+Package: samtools-examples
+Architecture: all
+Depends: ${misc:Depends}
+Description: examples
+ .............

Modified: trunk/packages/samtools/trunk/debian/copyright
===================================================================
--- trunk/packages/samtools/trunk/debian/copyright	2009-07-09 13:42:46 UTC (rev 3602)
+++ trunk/packages/samtools/trunk/debian/copyright	2009-07-10 09:38:27 UTC (rev 3603)
@@ -1,4 +1,11 @@
+Machine-readable license summary, see ‘http://dep.debian.net/deps/dep5/’.
 
+Name    :  
+Contact :  
+Source  :  http://downloads.sourceforge.net/sourceforge/samtools/samtools-0.1.5c.tar.bz2
+
+
+
 ./bgzf.c: * Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
 ./bgzip.c: * Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
 
@@ -23,8 +30,3 @@
  AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-
-Files: debian/*
-Copyright: © 2009, Charles Plessy <plessy at debian.org> and
-License: Same as SAMtools
- See above.

Deleted: trunk/packages/samtools/trunk/debian/docs
===================================================================
--- trunk/packages/samtools/trunk/debian/docs	2009-07-09 13:42:46 UTC (rev 3602)
+++ trunk/packages/samtools/trunk/debian/docs	2009-07-10 09:38:27 UTC (rev 3603)
@@ -1 +0,0 @@
-NEWS

Deleted: trunk/packages/samtools/trunk/debian/install
===================================================================
--- trunk/packages/samtools/trunk/debian/install	2009-07-09 13:42:46 UTC (rev 3602)
+++ trunk/packages/samtools/trunk/debian/install	2009-07-10 09:38:27 UTC (rev 3603)
@@ -1,3 +0,0 @@
-bgzip	usr/bin
-razip	usr/bin
-samtools	usr/bin

Added: trunk/packages/samtools/trunk/debian/libbam-dev.install
===================================================================
--- trunk/packages/samtools/trunk/debian/libbam-dev.install	                        (rev 0)
+++ trunk/packages/samtools/trunk/debian/libbam-dev.install	2009-07-10 09:38:27 UTC (rev 3603)
@@ -0,0 +1 @@
+libbam.a	usr/lib

Deleted: trunk/packages/samtools/trunk/debian/manpages
===================================================================
--- trunk/packages/samtools/trunk/debian/manpages	2009-07-09 13:42:46 UTC (rev 3602)
+++ trunk/packages/samtools/trunk/debian/manpages	2009-07-10 09:38:27 UTC (rev 3603)
@@ -1 +0,0 @@
-samtools.1

Added: trunk/packages/samtools/trunk/debian/reference
===================================================================
--- trunk/packages/samtools/trunk/debian/reference	                        (rev 0)
+++ trunk/packages/samtools/trunk/debian/reference	2009-07-10 09:38:27 UTC (rev 3603)
@@ -0,0 +1,12 @@
+ at article{HengLi06082009,
+author = {Li, Heng and Handsaker, Bob and Wysoker, Alec and Fennell, Tim and Ruan, Jue and Homer, Nils and Marth, Gabor and Abecasis, Goncalo and Durbin, Richard and 1000 Genome Project Data Processing Subgroup,  },
+title = {{The Sequence Alignment/Map (SAM) Format and SAMtools}},
+journal = {Bioinformatics},
+volume = {},
+number = {},
+pages = {btp352},
+doi = {10.1093/bioinformatics/btp352},
+year = {2009},
+URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btp352v1},
+eprint = {http://bioinformatics.oxfordjournals.org/cgi/reprint/btp352v1.pdf}
+}

Modified: trunk/packages/samtools/trunk/debian/rules
===================================================================
--- trunk/packages/samtools/trunk/debian/rules	2009-07-09 13:42:46 UTC (rev 3602)
+++ trunk/packages/samtools/trunk/debian/rules	2009-07-10 09:38:27 UTC (rev 3603)
@@ -3,3 +3,5 @@
 include /usr/share/cdbs/1/rules/debhelper.mk
 include /usr/share/cdbs/1/class/makefile.mk
 
+DEB_MAKE_BUILD_TARGET = all razip lib
+DEB_MAKE_CHECK_TARGET = -C examples all

Added: trunk/packages/samtools/trunk/debian/samtools-examples.examples
===================================================================
--- trunk/packages/samtools/trunk/debian/samtools-examples.examples	                        (rev 0)
+++ trunk/packages/samtools/trunk/debian/samtools-examples.examples	2009-07-10 09:38:27 UTC (rev 3603)
@@ -0,0 +1,3 @@
+examples/ex1.bam
+examples/ex1.fa
+examples/00README.txt

Copied: trunk/packages/samtools/trunk/debian/samtools.docs (from rev 3602, trunk/packages/samtools/trunk/debian/docs)
===================================================================
--- trunk/packages/samtools/trunk/debian/samtools.docs	                        (rev 0)
+++ trunk/packages/samtools/trunk/debian/samtools.docs	2009-07-10 09:38:27 UTC (rev 3603)
@@ -0,0 +1,2 @@
+debian/reference
+NEWS


Property changes on: trunk/packages/samtools/trunk/debian/samtools.docs
___________________________________________________________________
Added: svn:mergeinfo
   + 

Copied: trunk/packages/samtools/trunk/debian/samtools.install (from rev 3602, trunk/packages/samtools/trunk/debian/install)
===================================================================
--- trunk/packages/samtools/trunk/debian/samtools.install	                        (rev 0)
+++ trunk/packages/samtools/trunk/debian/samtools.install	2009-07-10 09:38:27 UTC (rev 3603)
@@ -0,0 +1,3 @@
+#bgzip	usr/bin
+razip	usr/bin
+samtools	usr/bin


Property changes on: trunk/packages/samtools/trunk/debian/samtools.install
___________________________________________________________________
Added: svn:mergeinfo
   + 

Copied: trunk/packages/samtools/trunk/debian/samtools.manpages (from rev 3602, trunk/packages/samtools/trunk/debian/manpages)
===================================================================
--- trunk/packages/samtools/trunk/debian/samtools.manpages	                        (rev 0)
+++ trunk/packages/samtools/trunk/debian/samtools.manpages	2009-07-10 09:38:27 UTC (rev 3603)
@@ -0,0 +1 @@
+samtools.1


Property changes on: trunk/packages/samtools/trunk/debian/samtools.manpages
___________________________________________________________________
Added: svn:mergeinfo
   +

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