From: Charles Plessy <plessy@debian.org>
Date: Tue, 12 Apr 2011 05:57:33 +0000 (+0900)
Subject: Merge commit 'upstream/0.2.4'
X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=tabix.git;a=commitdiff_plain;h=6154f20a217dfc124ef3016ba6adccd709c00f29;hp=2112b1dba17e822d8028151605b4cdc01f0a4c3d

Merge commit 'upstream/0.2.4'
---

diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..f5d91ed
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+tabix (0.2.3-1) unstable; urgency=low
+
+  * Initial release (Closes: #606446)
+
+ -- Charles Plessy <plessy@debian.org>  Wed, 19 Jan 2011 22:16:39 +0900
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..45a4fb7
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+8
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..ba4bc77
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,22 @@
+Source: tabix
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Charles Plessy <plessy@debian.org>
+Build-Depends: cdbs, debhelper (>= 8), zlib1g-dev
+Standards-Version: 3.9.1
+Homepage: http://samtools.sourceforge.net/tabix.shtml
+Vcs-Git: git://git.debian.org/debian-med/tabix.git
+Vcs-Browser: http://git.debian.org/?p=debian-med/tabix.git
+
+Package: tabix
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: generic indexer for TAB-delimited genome position files
+ Tabix indexes files where some columns indicate sequence coordinates: name
+ (usually a chromosme), start and stop. The input data file must be position
+ sorted and compressed by bgzip (provided in this package), which has a gzip
+ like interface. After indexing, tabix is able to quickly retrieve data lines by
+ chromosomal coordinates. Fast data retrieval also works over network if an URI
+ is given as a file name.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..d70fecf
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,26 @@
+Format: DEP-5
+Source: http://sourceforge.net/projects/samtools/files/tabix/tabix-0.2.3.tar.bz2
+Copyright: © 2008 Genome Research Ltd (GRL).
+ © 2008 Broad Institute / Massachusetts Institute of Technology
+ © 2009 Genome Research Ltd (GRL), 2010 Broad Institute
+ © 2010 Broad Institute.
+License: MIT
+ Permission is hereby granted, free of charge, to any person obtaining
+ a copy of this software and associated documentation files (the
+ "Software"), to deal in the Software without restriction, including
+ without limitation the rights to use, copy, modify, merge, publish,
+ distribute, sublicense, and/or sell copies of the Software, and to
+ permit persons to whom the Software is furnished to do so, subject to
+ the following conditions:
+ .
+ The above copyright notice and this permission notice shall be
+ included in all copies or substantial portions of the Software.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ NONINFRINGEMENT. IN NO EVENT SHALL THE 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 THE
+ SOFTWARE.
diff --git a/debian/docs b/debian/docs
new file mode 100644
index 0000000..edc0071
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1 @@
+NEWS
diff --git a/debian/examples b/debian/examples
new file mode 100644
index 0000000..0fbb01d
--- /dev/null
+++ b/debian/examples
@@ -0,0 +1,2 @@
+example.gtf.gz
+example.gtf.gz.tbi
diff --git a/debian/install b/debian/install
new file mode 100644
index 0000000..431c734
--- /dev/null
+++ b/debian/install
@@ -0,0 +1,2 @@
+tabix	usr/bin
+bgzip	usr/bin
diff --git a/debian/links b/debian/links
new file mode 100644
index 0000000..f8f82ba
--- /dev/null
+++ b/debian/links
@@ -0,0 +1 @@
+/usr/share/man/man1/tabix.1.gz /usr/share/man/man1/bgzip.1.gz
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..bb616e0
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+tabix.1
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..dd55160
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,6 @@
+#!/usr/bin/make -f
+
+include /usr/share/cdbs/1/rules/debhelper.mk
+include /usr/share/cdbs/1/class/makefile.mk
+
+DEB_COMPRESS_EXCLUDE  = .tbi
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..7aa6ef3
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,4 @@
+version=3
+opts=downloadurlmangle=s/\/download// \
+  http://sourceforge.net/projects/samtools/files/tabix/ \
+  http://sourceforge.net/projects/samtools/files/tabix/tabix-(.*).tar.bz2/download