[med-svn] [grabix] 01/11: 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.
Andreas Tille
tille at debian.org
Thu Dec 7 18:56:21 UTC 2017
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tille pushed a commit to branch master
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commit f1d75f9119c8640f159e6f70cada376c3c267fd6
Author: Steffen Moeller <moeller at debian.org>
Date: Thu Jul 18 14:15:47 2013 +0000
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.
---
debian/README.Debian | 8 +++++++
debian/changelog | 5 +++++
debian/compat | 1 +
debian/control | 29 ++++++++++++++++++++++++
debian/copyright | 36 +++++++++++++++++++++++++++++
debian/docs | 1 +
debian/grabix.1 | 51 ++++++++++++++++++++++++++++++++++++++++++
debian/grabix.install | 1 +
debian/manpages | 1 +
debian/patches/Hardening.patch | 13 +++++++++++
debian/patches/series | 1 +
debian/rules | 18 +++++++++++++++
debian/source/format | 1 +
13 files changed, 166 insertions(+)
diff --git a/debian/README.Debian b/debian/README.Debian
new file mode 100644
index 0000000..05fe611
--- /dev/null
+++ b/debian/README.Debian
@@ -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 <moeller at debian.org> Thu, 18 Jul 2013 14:45:55 +0200
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..5ee3153
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+grabix (0.0~git20130718-1) unstable; urgency=low
+
+ * Initial release.
+
+ -- Steffen Moeller <moeller at debian.org> Thu, 18 Jul 2013 14:45:55 +0200
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..50646df
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,29 @@
+Source: grabix
+Section: science
+Priority: extra
+Maintainer: Steffen Moeller <moeller at debian.org>
+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.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..611f547
--- /dev/null
+++ b/debian/copyright
@@ -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 <moeller at debian.org>
+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.
diff --git a/debian/docs b/debian/docs
new file mode 100644
index 0000000..b43bf86
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1 @@
+README.md
diff --git a/debian/grabix.1 b/debian/grabix.1
new file mode 100644
index 0000000..fa9e1ca
--- /dev/null
+++ b/debian/grabix.1
@@ -0,0 +1,51 @@
+.\" Hey, EMACS: -*- nroff -*-
+.\" (C) Copyright 2013 Steffen Moeller <moeller at debian.org>,
+.\"
+.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
diff --git a/debian/grabix.install b/debian/grabix.install
new file mode 100644
index 0000000..1e29fa1
--- /dev/null
+++ b/debian/grabix.install
@@ -0,0 +1 @@
+grabix usr/bin
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..19ee710
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/grabix.1
diff --git a/debian/patches/Hardening.patch b/debian/patches/Hardening.patch
new file mode 100644
index 0000000..3b6c4fe
--- /dev/null
+++ b/debian/patches/Hardening.patch
@@ -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
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..547c0fb
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+Hardening.patch
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..1281061
--- /dev/null
+++ b/debian/rules
@@ -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 $@
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)
--
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