[med-svn] [smrtanalysis] 02/02: initial commit

[Afif Elghraoui]

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afif-guest pushed a commit to branch master
in repository smrtanalysis.

commit 2585aa3cd79c858881363352e41b58c8b33ef3e0
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Sun Jun 7 02:18:31 2015 -0700

    initial commit
---
 debian/changelog     |  5 +++++
 debian/compat        |  1 +
 debian/control       | 42 ++++++++++++++++++++++++++++++++++++++++++
 debian/copyright     | 37 +++++++++++++++++++++++++++++++++++++
 debian/rules         |  6 ++++++
 debian/source/format |  1 +
 6 files changed, 92 insertions(+)

diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..f00a5ce
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+smrtanalysis (2.3.0-1) UNRELEASED; urgency=low
+
+  * Initial release (Closes: #nnnn)
+
+ -- Afif Elghraoui <afif at ghraoui.name>  Sun, 07 Jun 2015 01:48:30 -0700
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..79a0ddc
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,42 @@
+Source: smrtanalysis
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Afif Elghraoui <afif at ghraoui.name>
+Build-Depends: debhelper (>= 9)
+Standards-Version: 3.9.6
+Homepage: https://github.com/PacificBiosciences/SMRT-Analysis
+Vcs-Git: git://anonscm.debian.org/debian-med/smrtanalysis.git
+Vcs-Browser: http://anonscm.debian.org/cgit/smrtanalysis.git
+
+Package: smrtanalysis
+Architecture: all
+Depends: ${misc:Depends},
+	 python-pbcore,
+	 python-pbh5tools
+Description: software suite for single molecule, real-time sequencing
+ SMRT® Analysis is a powerful, open-source bioinformatics software suite
+ available for analysis of DNA sequencing data from Pacific Biosciences’
+ SMRT technology.
+ .
+ Users can choose from a variety of analysis protocols that utilize PacBio®
+ and third-party tools. Analysis protocols include de novo genome assembly,
+ cDNA mapping, DNA base-modification detection, and long-amplicon analysis to
+ determine phased consensus sequences.
+ .
+ This is a metapackage that depends on the components of SMRT Analysis.
+
+Package: smrtportal
+Architecture: all
+Depends: smrtanalysis,
+	 ${misc:Depends}
+Description: web interface for smrtanalysis
+ The browser-based SMRT Portal GUI offers push-button analysis, allowing the
+ user to create, submit, and monitor analysis jobs. The underlying algorithms
+ can be accessed on the command-line for pipeline development with SMRT Pipe,
+ utilizing LIMS-friendly APIs and a large collection of utilities for working
+ with PacBio bas.h5 files and other common file formats. SMRT View is an
+ application for graphical visualization of processed and annotated sequence
+ data, including kinetics data unique to PacBio SMRT technology.
+ .
+ This is a metapackage that depends on the components of SMRT Portal.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..a5de49a
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,37 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: SMRTAnalysis
+Upstream-Contact: Pacific Biosciences <devnet at pacificbiosciences.com>
+Source: http://pacbiodevnet.com
+
+Files: *
+Copyright: 2013-2015 Pacific Biosciences of California, Inc.
+License: BSD-3-Clause
+
+Files: debian/*
+Copyright: 2015 Afif Elghraoui <afif at ghraoui.name>
+License: BSD-3-Clause
+
+License: BSD-3-Clause
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+ 1. Redistributions of source code must retain the above copyright
+    notice, this list of conditions and the following disclaimer.
+ 2. Redistributions in binary form must reproduce the above copyright
+    notice, this list of conditions and the following disclaimer in the
+    documentation and/or other materials provided with the distribution.
+ 3. Neither the name of the University nor the names of its contributors
+    may be used to endorse or promote products derived from this software
+    without specific prior written permission.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT 
+ LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR 
+ A PARTICULAR PURPOSE ARE DISCLAIMED.  IN NO EVENT SHALL THE HOLDERS OR
+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, 
+ EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, 
+ PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR 
+ PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF 
+ LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING 
+ NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 
+ SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..28d4ce9
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,6 @@
+#!/usr/bin/make -f
+
+include /usr/share/dpkg/default.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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