From: Charles Plessy Date: Sat, 7 May 2011 12:17:57 +0000 (+0900) Subject: Merge commit 'upstream/0.2.5' X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=tabix.git;a=commitdiff_plain;h=6ef84accd7e4c5a48a7a959475bc1e5934e8adeb;hp=aefb3dc25b66447517ef917ffa68cacd5821cf0d Merge commit 'upstream/0.2.5' --- diff --git a/debian/changelog b/debian/changelog new file mode 100644 index 0000000..b7ec553 --- /dev/null +++ b/debian/changelog @@ -0,0 +1,13 @@ +tabix (0.2.4-1) unstable; urgency=low + + * New upstream release. + * Incremented Standards-Version to reflect conformance with Policy 3.9.2 + (debian/control). + + -- Charles Plessy Tue, 12 Apr 2011 17:15:33 +0900 + +tabix (0.2.3-1) unstable; urgency=low + + * Initial release (Closes: #606446) + + -- Charles Plessy 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..9692efd --- /dev/null +++ b/debian/control @@ -0,0 +1,22 @@ +Source: tabix +Section: science +Priority: optional +Maintainer: Debian Med Packaging Team +DM-Upload-Allowed: yes +Uploaders: Charles Plessy +Build-Depends: cdbs, debhelper (>= 8), zlib1g-dev +Standards-Version: 3.9.2 +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..c646d42 --- /dev/null +++ b/debian/copyright @@ -0,0 +1,34 @@ +Format: http://dep.debian.net/deps/dep5/ +Source: http://sourceforge.net/projects/samtools/files/tabix/tabix-0.2.4.tar.bz2 + +Files: * +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 + +Files: python/* +Copyright: © 2011 Seoul National University. +License: MIT + +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..f92ecf9 --- /dev/null +++ b/debian/watch @@ -0,0 +1,4 @@ +version=3 +opts=downloadurlmangle=s/\/download//,filenamemangle=s/http...sourceforge.net.projects.samtools.files.tabix.//;s/.download// \ + http://sourceforge.net/projects/samtools/files/tabix/ \ + http://sourceforge.net/projects/samtools/files/tabix/tabix-(.*).tar.bz2/download