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commit 24c9db3744dd881aa6a8c1cfc780b130f8ad4a0b Author: Andreas Tille <ti...@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-packag...@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-packag...@lists.alioth.debian.org> +Uploaders: Andreas Tille <ti...@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 <ti...@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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/contrafold.git _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit