[med-svn] [contrafold] 02/02: Add debian packaging but there are C++ errors
Andreas Tille
tille at debian.org
Thu Sep 15 07:25:54 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository contrafold.
commit 24c9db3744dd881aa6a8c1cfc780b130f8ad4a0b
Author: Andreas Tille <tille at debian.org>
Date: Thu Sep 15 09:24:47 2016 +0200
Add debian packaging but there are C++ errors
---
debian/changelog | 5 +++++
debian/compat | 1 +
debian/control | 38 ++++++++++++++++++++++++++++++++++++++
debian/copyright | 38 ++++++++++++++++++++++++++++++++++++++
debian/doc-base | 30 ++++++++++++++++++++++++++++++
debian/rules | 6 ++++++
debian/source/format | 1 +
debian/upstream/metadata | 12 ++++++++++++
debian/watch | 4 ++++
9 files changed, 135 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..2affeb4
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+contrafold (2.02-1) UNRELEASED; urgency=medium
+
+ * Initial release (Closes: #<bug>)
+
+ -- DMPT <debian-med-packaging at lists.alioth.debian.org> Thu, 15 Sep 2016 08:59:54 +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..1307980
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,38 @@
+Source: contrafold
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
+Build-Depends: debhelper (>= 9)
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/contrafold.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/contrafold.git
+Homepage: http://contra.stanford.edu/contrafold/
+
+Package: contrafold
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: CONditional TRAining for RNA Secondary Structure Prediction
+ For several decades, free energy minimization methods have been the dominant
+ strategy for single sequence RNA secondary structure prediction. More
+ recently, stochastic context-free grammars (SCFGs) have emerged as an
+ alternative probabilistic methodology for modeling RNA structure. Unlike
+ physics-based methods, which rely on thousands of experimentally-measured
+ thermodynamic parameters, SCFGs use fully-automated statistical learning
+ algorithms to derive model parameters. Despite this advantage, however,
+ probabilistic methods have not replaced free energy minimization methods as
+ the tool of choice for secondarystructure prediction, as the accuracies of
+ the best current SCFGs have yet to match those of the best physics-based
+ models.
+ .
+ CONTRAfold is a novel secondary structure prediction method based on
+ conditional log-linear models (CLLMs), a flexible class of probabilistic
+ models which generalize upon SCFGs by using discriminative training and
+ feature-rich scoring. By incorporating most of the features found in
+ typical thermodynamic models, CONTRAfold achieves the highest single
+ sequence prediction accuracies to date, outperforming currently available
+ probabilistic and physics-based techniques. Our result thus closes the gap
+ between probabilistic and thermodynamic models, demonstrating that
+ statistical learning procedures provide an effective alternative to
+ empirical measurement of thermodynamic parameters for RNA secondary
+ structure prediction.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..c3d2426
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,38 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: CONTRAfold
+Source: http://contra.stanford.edu/contrafold/download.html
+
+Files: *
+Copyright: 2005-2008 Chuong B. Do and Daniel A. Woods1 and Serafim Batzoglou
+License: BSD-3-Clause
+
+Files: debian/*
+Copyright: 2016 Andreas Tille <tille at debian.org>
+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:
+ .
+ * Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+ * 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.
+ * Neither the name of Stanford 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 COPYRIGHT
+ OWNER 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/doc-base b/debian/doc-base
new file mode 100644
index 0000000..1276304
--- /dev/null
+++ b/debian/doc-base
@@ -0,0 +1,30 @@
+Document: contrafold
+Title: RNA secondary structure prediction without physics-based models
+Author: Chuong B. Do and Daniel A. Woods1 and Serafim Batzoglou
+Abstract: CONditional TRAining for RNA Secondary Structure Prediction
+ For several decades, free energy minimization methods have been the dominant
+ strategy for single sequence RNA secondary structure prediction. More
+ recently, stochastic context-free grammars (SCFGs) have emerged as an
+ alternative probabilistic methodology for modeling RNA structure. Unlike
+ physics-based methods, which rely on thousands of experimentally-measured
+ thermodynamic parameters, SCFGs use fully-automated statistical learning
+ algorithms to derive model parameters. Despite this advantage, however,
+ probabilistic methods have not replaced free energy minimization methods as
+ the tool of choice for secondarystructure prediction, as the accuracies of
+ the best current SCFGs have yet to match those of the best physics-based
+ models.
+ .
+ CONTRAfold is a novel secondary structure prediction method based on
+ conditional log-linear models (CLLMs), a flexible class of probabilistic
+ models which generalize upon SCFGs by using discriminative training and
+ feature-rich scoring. By incorporating most of the features found in
+ typical thermodynamic models, CONTRAfold achieves the highest single
+ sequence prediction accuracies to date, outperforming currently available
+ probabilistic and physics-based techniques. Our result thus closes the gap
+ between probabilistic and thermodynamic models, demonstrating that
+ statistical learning procedures provide an effective alternative to
+ empirical measurement of thermodynamic parameters for RNA secondary
+ structure prediction.
+Section: Science/Biology
+
+Files: /usr/share/doc/contrafold/manual.pdf
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..fc73626
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,6 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+
+%:
+ dh $@ --sourcedirectory=src
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..c2bcc1a
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,12 @@
+Reference:
+ Author: Chuong B. Do and Daniel A. Woods1 and Serafim Batzoglou
+ Title: "CONTRAfold: RNA secondary structure prediction without physics-based models"
+ Journal: Bioinformatics
+ Year: 2006
+ Volume: 22
+ Number: 14
+ Pages: e90-e98
+ DOI: 10.1093/bioinformatics/btl246
+ PMID: 16873527
+ URL: http://bioinformatics.oxfordjournals.org/content/22/14/e90.abstract
+ eprint: http://bioinformatics.oxfordjournals.org/content/22/14/e90.full.pdf+html
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..9bbab19
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,4 @@
+version=3
+
+opts=uversionmangle=s/_/./g \
+ http://contra.stanford.edu/contrafold/download.html contrafold_v(\d[\d_.]+)\.tar\.gz
--
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