[med-svn] [crac] 02/02: Add initial debia/ dir as prepared by Antony
Andreas Tille
tille at debian.org
Wed Jul 9 08:33:40 UTC 2014
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository crac.
commit a23e21856605b9841bfbb0bb0a52170cfbbf5540
Author: Andreas Tille <tille at debian.org>
Date: Wed Jul 9 10:32:30 2014 +0200
Add initial debia/ dir as prepared by Antony
---
debian/README.Debian | 6 ++++++
debian/README.source | 10 ++++++++++
debian/changelog | 5 +++++
debian/compat | 1 +
debian/control | 31 +++++++++++++++++++++++++++++++
debian/copyright | 34 ++++++++++++++++++++++++++++++++++
debian/crac.doc-base.EX | 20 ++++++++++++++++++++
debian/crac.docs | 4 ++++
debian/info | 3 +++
debian/manpages | 1 +
debian/rules | 8 ++++++++
debian/source/format | 1 +
debian/upstream/metadata | 20 ++++++++++++++++++++
debian/watch | 3 +++
14 files changed, 147 insertions(+)
diff --git a/debian/README.Debian b/debian/README.Debian
new file mode 100644
index 0000000..626eab5
--- /dev/null
+++ b/debian/README.Debian
@@ -0,0 +1,6 @@
+crac for Debian
+---------------
+
+<possible notes regarding this package - if none, delete this file>
+
+ -- Anthony Boureux <Anthony.Boureux at gmail.com> Wed, 11 Jun 2014 09:47:48 +0200
diff --git a/debian/README.source b/debian/README.source
new file mode 100644
index 0000000..500381b
--- /dev/null
+++ b/debian/README.source
@@ -0,0 +1,10 @@
+crac for Debian
+---------------
+
+<this file describes information about the source package, see Debian policy
+manual section 4.14. You WILL either need to modify or delete this file>
+
+
+
+ -- Anthony Boureux <Anthony.Boureux at gmail.com> Wed, 11 Jun 2014 09:47:48 +0200
+
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..d0a56ad
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+crac (1.5.0-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #<bug>)
+
+ -- Anthony Boureux <Anthony.Boureux at gmail.com> Wed, 11 Jun 2014 09:47:48 +0200
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..ec63514
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+9
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..7396d5e
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,31 @@
+Source: crac
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Anthony Boureux <Anthony.Boureux at gmail.com>,
+ Andreas Tille <tille at debian.org>
+Build-Depends: debhelper (>= 9), autotools-dev, zlib1g-dev
+Standards-Version: 3.9.5
+Homepage: http://crac.gforge.inria.fr/
+Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/crac.git
+Vcs-Git: git://anonscm.debian.org/debian-med/crac.git
+
+Package: crac
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: integrated RNA-Seq read analysis
+ CRAC is a tool to analyze High Throughput Sequencing (HTS) data in
+ comparison to a reference genome. It is intended for transcriptomic
+ and genomic sequencing reads. More precisely, with transcriptomic
+ reads as input, it predicts point mutations, indels, splice junction,
+ and chimeric RNAs (ie, non colinear splice junctions). CRAC can also
+ output positions and nature of sequence error that it detects in the
+ reads. CRAC uses a genome index. This index must be computed before
+ running the read analysis. For this sake, use the command "crac-index"
+ on your genome files. You can then process the reads using the command
+ crac. See the man page of CRAC (help file) by typing "man crac". CRAC
+ requires large amount of main memory on your computer. For processing
+ against the Human genome, say 50 million reads of 100 nucleotide each,
+ CRAC requires about 40 gigabytes of main memory. Check whether the
+ system of your computing server is equipped with sufficient amount of
+ memory before launching an analysis.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..a3a2083
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,34 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: crac
+Source: http://crac.gforge.inria.fr
+
+Files: *
+Copyright: © 2012-2014 by Nicolas PHILIPPE <nicolas.philippe at lirmm.fr>
+ © 2012-2014 by Mikaël SALSON <mikael.salson at lifl.fr>
+ © 2012-2014 by Alban MANCHERON <alban.mancheron at lirmm.fr>
+ © 2013-2014 by Jérôme Audoux <Jerome.Audoux at gmail.com>
+License: CeCILL
+ <Put the license of the package here indented by 1 space>
+ <This follows the format of Description: lines in control file>
+ .
+ <Including paragraphs>
+
+Files: debian/*
+Copyright: 2014 Anthony Boureux <Anthony.Boureux at gmail.com>
+License: GPL-2+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
+
diff --git a/debian/crac.doc-base.EX b/debian/crac.doc-base.EX
new file mode 100644
index 0000000..e04a4a8
--- /dev/null
+++ b/debian/crac.doc-base.EX
@@ -0,0 +1,20 @@
+Document: crac
+Title: Debian crac Manual
+Author: <insert document author here>
+Abstract: This manual describes what crac is
+ and how it can be used to
+ manage online manuals on Debian systems.
+Section: unknown
+
+Format: debiandoc-sgml
+Files: /usr/share/doc/crac/crac.sgml.gz
+
+Format: postscript
+Files: /usr/share/doc/crac/crac.ps.gz
+
+Format: text
+Files: /usr/share/doc/crac/crac.text.gz
+
+Format: HTML
+Index: /usr/share/doc/crac/html/index.html
+Files: /usr/share/doc/crac/html/*.html
diff --git a/debian/crac.docs b/debian/crac.docs
new file mode 100644
index 0000000..be5a34a
--- /dev/null
+++ b/debian/crac.docs
@@ -0,0 +1,4 @@
+NEWS
+README
+#doc/crac.pdf
+#doc/crac.html/
diff --git a/debian/info b/debian/info
new file mode 100644
index 0000000..37fde8a
--- /dev/null
+++ b/debian/info
@@ -0,0 +1,3 @@
+doc/crac.info
+src/libGkArrays/doc/libGkArrays.info
+src/libGkArrays/src/libProgressBar-1.2.0/doc/libProgressBar.info
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..d44bd41
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+man/crac.1
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..c6d751b
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,8 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+%:
+ dh $@ --with autotools-dev
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/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..002c9e1
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,20 @@
+Archive: GForge
+FAQ: http://crac.gforge.inria.fr/index.php?id=faq
+Homepage: http://crac.gforge.inria.fr/
+Name: Crac is a tool to analyse RNA-Seq data provided by NGS
+Reference:
+ Article: PhilippeRivals23537109
+ Author: Philippe, Salson, Commes, Rivals
+ Title: "CRAC: an integrated approach to the analysis of RNA-seq reads"
+ Journal: Genome Biology
+ Volume: 14
+ Number: 3
+ Pages: R30
+ Year: 2013
+ DOI: 10.1186/gb-2013-14-3-r30
+ PMID: 23537109
+ URL: http://genomebiology.com/content/14/3/R30
+ Eprint: http://genomebiology.com/content/pdf/gb-2013-14-3-r30.pdf
+References: http://crac.gforge.inria.fr/
+Repository: https://gforge.inria.fr/frs/?group_id=3008
+Repository-Browse: https://gforge.inria.fr/frs/?group_id=3008
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..b2d320f
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=3
+
+https://gforge.inria.fr/frs/?group_id=3008 .*/crac-(.*)\.tar\.gz
--
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