Author: moeller Date: 2013-07-18 14:15:47 +0000 (Thu, 18 Jul 2013) New Revision: 14179
Added: trunk/packages/grabix/ trunk/packages/grabix/trunk/ trunk/packages/grabix/trunk/debian/ trunk/packages/grabix/trunk/debian/README.Debian trunk/packages/grabix/trunk/debian/changelog trunk/packages/grabix/trunk/debian/compat trunk/packages/grabix/trunk/debian/control trunk/packages/grabix/trunk/debian/copyright trunk/packages/grabix/trunk/debian/docs trunk/packages/grabix/trunk/debian/grabix.1 trunk/packages/grabix/trunk/debian/grabix.install trunk/packages/grabix/trunk/debian/manpages trunk/packages/grabix/trunk/debian/patches/ trunk/packages/grabix/trunk/debian/patches/Hardening.patch trunk/packages/grabix/trunk/debian/patches/series trunk/packages/grabix/trunk/debian/rules trunk/packages/grabix/trunk/debian/source/ trunk/packages/grabix/trunk/debian/source/format Log: The grabix tools know how to work on compressed files from next generation sequencing. The GEMINI suite for SNP priorisation has it as a dependency. Property changes on: trunk/packages/grabix/trunk/debian ___________________________________________________________________ Added: mergeWithUpstream + 1 Added: trunk/packages/grabix/trunk/debian/README.Debian =================================================================== --- trunk/packages/grabix/trunk/debian/README.Debian (rev 0) +++ trunk/packages/grabix/trunk/debian/README.Debian 2013-07-18 14:15:47 UTC (rev 14179) @@ -0,0 +1,8 @@ +grabix for Debian +----------------- + +The motivation for this package is mostly as a redundancy for +GEMINI, a Python-based suite for analysing and priorising the +variations found in next generation sequencing data. + + -- Steffen Moeller <[email protected]> Thu, 18 Jul 2013 14:45:55 +0200 Added: trunk/packages/grabix/trunk/debian/changelog =================================================================== --- trunk/packages/grabix/trunk/debian/changelog (rev 0) +++ trunk/packages/grabix/trunk/debian/changelog 2013-07-18 14:15:47 UTC (rev 14179) @@ -0,0 +1,5 @@ +grabix (0.0~git20130718-1) unstable; urgency=low + + * Initial release. + + -- Steffen Moeller <[email protected]> Thu, 18 Jul 2013 14:45:55 +0200 Added: trunk/packages/grabix/trunk/debian/compat =================================================================== --- trunk/packages/grabix/trunk/debian/compat (rev 0) +++ trunk/packages/grabix/trunk/debian/compat 2013-07-18 14:15:47 UTC (rev 14179) @@ -0,0 +1 @@ +8 Added: trunk/packages/grabix/trunk/debian/control =================================================================== --- trunk/packages/grabix/trunk/debian/control (rev 0) +++ trunk/packages/grabix/trunk/debian/control 2013-07-18 14:15:47 UTC (rev 14179) @@ -0,0 +1,29 @@ +Source: grabix +Section: science +Priority: extra +Maintainer: Steffen Moeller <[email protected]> +Build-Depends: debhelper (>= 8.0.0) +Standards-Version: 3.9.4 +Homepage: https://github.com/arq5x/grabix +#Vcs-Git: git://git.debian.org/collab-maint/grabix.git +#Vcs-Browser: http://git.debian.org/?p=collab-maint/grabix.git;a=summary + +Package: grabix +Architecture: any +Depends: ${shlibs:Depends}, ${misc:Depends} +Description: wee tool for random access into BGZF files + In biomedical research it is increasing practice to study + the genetic basis of disease. This now frequently comprises + the sequencing of human sequences. The output of the machine + however is redundant, and the real sequence is the best + sequence to explain the redundancy. The exchange of data + happens only with compressed files - to huge and redundant + to perform otherwise. One should avoid uncompression whenever + possible. + . + grabix leverages the fantastic BGZF library of the samtools + package to provide random access into text files that have + been compressed with bgzip. grabix creates it's own index + (.gbi) of the bgzipped file. Once indexed, one can extract + arbitrary lines from the file with the grab command. Or + choose random lines with the, well, random command. Added: trunk/packages/grabix/trunk/debian/copyright =================================================================== --- trunk/packages/grabix/trunk/debian/copyright (rev 0) +++ trunk/packages/grabix/trunk/debian/copyright 2013-07-18 14:15:47 UTC (rev 14179) @@ -0,0 +1,36 @@ +Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: grabix +Source: <url://example.com> + +Files: * +Copyright: <years> <put author's name and email here> + <years> <likewise for another author> +License: MIT + +Files: debian/* +Copyright: 2013 Steffen Moeller <[email protected]> +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. + +# Please also look if there are files or directories which have a +# different copyright/license attached and list them here. +# Please avoid to pick license terms that are more restrictive than the +# packaged work, as it may make Debian's contributions unacceptable upstream. Added: trunk/packages/grabix/trunk/debian/docs =================================================================== --- trunk/packages/grabix/trunk/debian/docs (rev 0) +++ trunk/packages/grabix/trunk/debian/docs 2013-07-18 14:15:47 UTC (rev 14179) @@ -0,0 +1 @@ +README.md Added: trunk/packages/grabix/trunk/debian/grabix.1 =================================================================== --- trunk/packages/grabix/trunk/debian/grabix.1 (rev 0) +++ trunk/packages/grabix/trunk/debian/grabix.1 2013-07-18 14:15:47 UTC (rev 14179) @@ -0,0 +1,51 @@ +.\" Hey, EMACS: -*- nroff -*- +.\" (C) Copyright 2013 Steffen Moeller <[email protected]>, +.\" +.TH GRABIX SECTION "July 18, 2013" +.\" Please adjust this date whenever revising the manpage. +.\" +.\" Some roff macros, for reference: +.\" .nh disable hyphenation +.\" .hy enable hyphenation +.\" .ad l left justify +.\" .ad b justify to both left and right margins +.\" .nf disable filling +.\" .fi enable filling +.\" .br insert line break +.\" .sp <n> insert n+1 empty lines +.\" for manpage-specific macros, see man(7) +.SH NAME +grabix \- program to do something +.SH SYNOPSIS +.B bgzip +.RI bedfile +.br +.B grabix +index +.RI bedfile.gz +.br +.B grabix +grab +.RI bedfile.gz +.RI linenumber + +.SH DESCRIPTION +.PP +In biomedical research it is increasing practice to study +the genetic basis of disease. This now frequently comprises +the sequencing of human sequences. The output of the machine +however is redundant, and the real sequence is the best +sequence to explain the redundancy. The exchange of data +happens only with compressed files - to huge and redundant +to perform otherwise. One should avoid uncompression whenever +possible. +.PP +grabix leverages the fantastic BGZF library of the samtools +package to provide random access into text files that have +been compressed with bgzip. grabix creates it's own index +(.gbi) of the bgzipped file. Once indexed, one can extract +arbitrary lines from the file with the grab command. Or +choose random lines with the, well, random command. + +.SH SEE ALSO +.BR https://github.com/arq5x/grabix Added: trunk/packages/grabix/trunk/debian/grabix.install =================================================================== --- trunk/packages/grabix/trunk/debian/grabix.install (rev 0) +++ trunk/packages/grabix/trunk/debian/grabix.install 2013-07-18 14:15:47 UTC (rev 14179) @@ -0,0 +1 @@ +grabix usr/bin Added: trunk/packages/grabix/trunk/debian/manpages =================================================================== --- trunk/packages/grabix/trunk/debian/manpages (rev 0) +++ trunk/packages/grabix/trunk/debian/manpages 2013-07-18 14:15:47 UTC (rev 14179) @@ -0,0 +1 @@ +debian/grabix.1 Added: trunk/packages/grabix/trunk/debian/patches/Hardening.patch =================================================================== --- trunk/packages/grabix/trunk/debian/patches/Hardening.patch (rev 0) +++ trunk/packages/grabix/trunk/debian/patches/Hardening.patch 2013-07-18 14:15:47 UTC (rev 14179) @@ -0,0 +1,13 @@ +Index: grabix-0.0~git20130718/Makefile +=================================================================== +--- grabix-0.0~git20130718.orig/Makefile ++++ grabix-0.0~git20130718/Makefile +@@ -1,2 +1,7 @@ ++LDFLAGS+= -lstdc++ -lz ++CFLAGS+=-Wall + all: +- gcc -Wall -O2 -o grabix grabix.cpp bgzf.c -lstdc++ -lz ++ gcc $(CFLAGS) -o grabix grabix.cpp bgzf.c $(LDFLAGS) ++ ++clean: ++ rm -f grabix Added: trunk/packages/grabix/trunk/debian/patches/series =================================================================== --- trunk/packages/grabix/trunk/debian/patches/series (rev 0) +++ trunk/packages/grabix/trunk/debian/patches/series 2013-07-18 14:15:47 UTC (rev 14179) @@ -0,0 +1 @@ +Hardening.patch Added: trunk/packages/grabix/trunk/debian/rules =================================================================== --- trunk/packages/grabix/trunk/debian/rules (rev 0) +++ trunk/packages/grabix/trunk/debian/rules 2013-07-18 14:15:47 UTC (rev 14179) @@ -0,0 +1,18 @@ +#!/usr/bin/make -f +# -*- makefile -*- +# Sample debian/rules that uses debhelper. +# This file was originally written by Joey Hess and Craig Small. +# As a special exception, when this file is copied by dh-make into a +# dh-make output file, you may use that output file without restriction. +# This special exception was added by Craig Small in version 0.37 of dh-make. + +# Uncomment this to turn on verbose mode. +#export DH_VERBOSE=1 + +# Set default flags with dpkg-buildflags +export DEB_BUILD_MAINT_OPTIONS = hardening=+all +DPKG_EXPORT_BUILDFLAGS = 1 +include /usr/share/dpkg/buildflags.mk + +%: + dh $@ Property changes on: trunk/packages/grabix/trunk/debian/rules ___________________________________________________________________ Added: svn:executable + * Added: trunk/packages/grabix/trunk/debian/source/format =================================================================== --- trunk/packages/grabix/trunk/debian/source/format (rev 0) +++ trunk/packages/grabix/trunk/debian/source/format 2013-07-18 14:15:47 UTC (rev 14179) @@ -0,0 +1 @@ +3.0 (quilt) _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
