[med-svn] [smrtanalysis] 02/02: initial commit
This is an automated email from the git hooks/post-receive script.
afif-guest pushed a commit to branch master
in repository smrtanalysis.
commit 2585aa3cd79c858881363352e41b58c8b33ef3e0
Author: Afif Elghraoui a...@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 000..f00a5ce
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+smrtanalysis (2.3.0-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #)
+
+ -- Afif Elghraoui a...@ghraoui.name Sun, 07 Jun 2015 01:48:30 -0700
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 000..ec63514
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+9
diff --git a/debian/control b/debian/control
new file mode 100644
index 000..79a0ddc
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,42 @@
+Source: smrtanalysis
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team
debian-med-packag...@lists.alioth.debian.org
+Uploaders: Afif Elghraoui a...@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 000..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 dev...@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 a...@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
[med-svn] [smrtanalysis] 02/02: Initial commit
This is an automated email from the git hooks/post-receive script.
afif-guest pushed a commit to branch master
in repository smrtanalysis.
commit 2ba5b2f4df2cf782028d5706e636ae75737ee3fd
Author: Afif Elghraoui a...@ghraoui.name
Date: Sat May 16 15:05:32 2015 -0700
Initial commit
---
debian/README.source | 14 ++
debian/changelog | 5 +
debian/compat | 1 +
debian/control | 39 +++
debian/copyright | 36
debian/docs| 3 +++
debian/get-orig-source | 39 +++
debian/rules | 33 +
debian/source/format | 1 +
9 files changed, 171 insertions(+)
diff --git a/debian/README.source b/debian/README.source
new file mode 100644
index 000..dd8e8c8
--- /dev/null
+++ b/debian/README.source
@@ -0,0 +1,14 @@
+smrtanalysis for Debian
+---
+
+Pacific Biosciences distributes the SMRT Analysis suite releases on
+http://www.pacb.com/devnet/. The components are in various Github
+repositories at https://github.com/PacificBiosciences. The top-level
+SMRT Analysis repository there is used as the source for this package,
+but it contains only documentation.
+
+License information is in the main release and also in the subcomponents'
+repositories.
+
+ -- Afif Elghraoui a...@ghraoui.name, Sat, 16 May 2015 15:02:05 -0700
+
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 000..2d131c6
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+smrtanalysis (2.3.0-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #) is the bug number of your ITP
+
+ -- Afif Elghraoui a...@ghraoui.name Sat, 16 May 2015 00:13:48 -0700
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 000..ec63514
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+9
diff --git a/debian/control b/debian/control
new file mode 100644
index 000..edf671b
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,39 @@
+Source: smrtanalysis
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team
debian-med-packag...@lists.alioth.debian.org
+Uploaders: Afif Elghraoui a...@ghraoui.name
+Build-Depends: debhelper (= 9),
+ pandoc
+Standards-Version: 3.9.5
+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: ${misc:Depends}
+Description: software suite for single molecule, real-time sequencing
+ SMRT® Analysis is a powerful, open-source bioinformatics software suite
+ available for analysis of DNA sequencing data from Pacific Biosciences’
+ SMRT technology.
+ .
+ Users can choose from a variety of analysis protocols that utilize PacBio®
+ and third-party tools. Analysis protocols include de novo genome assembly,
+ cDNA mapping, DNA base-modification detection, and long-amplicon analysis to
+ determine phased consensus sequences.
+ .
+ This is a metapackage that depends on the components of SMRT Analysis
+
+Package: smrtportal
+Architecture: all
+Depends: smrtanalysis,
+${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.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 000..b215fa0
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,36 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: SMRT Analysis
+Source: https://github.com/PacificBiosciences/SMRT-Analysis
+
+Files: *
+Copyright: 2013-2015 Pacific Biosciences of California, Inc.
+License: BSD-3-Clause
+
+Files: debian/*
+Copyright: 2015 Afif Elghraoui a...@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
