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commit ec21345d2efdc9fdcd42c26c4d1e373f4f253c62 Author: Andreas Tille <[email protected]> Date: Mon May 28 15:32:50 2012 +0000 Take over information from tasks file into machine parseable code --- debian/changelog | 5 +++++ debian/compat | 1 + debian/control | 36 ++++++++++++++++++++++++++++++++++++ debian/copyright | 10 ++++++++++ debian/rules | 6 ++++++ debian/upstream | 20 ++++++++++++++++++++ 6 files changed, 78 insertions(+) diff --git a/debian/changelog b/debian/changelog new file mode 100644 index 0000000..a6aba20 --- /dev/null +++ b/debian/changelog @@ -0,0 +1,5 @@ +sap (1.1.1-1) unstable; urgency=low + + * Initial release + + -- Andreas Tille <[email protected]> Mon, 28 May 2012 17:14:53 +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..0b63901 --- /dev/null +++ b/debian/control @@ -0,0 +1,36 @@ +Source: sap +Section: science +Priority: optional +Maintainer: Debian Med Packaging Team <[email protected]> +DM-Upload-Allowed: yes +Uploaders: Andreas Tille <[email protected]> +Build-Depends: debhelper (>= 9) +Standards-Version: 3.9.3 +Homepage: http://mathbio.nimr.mrc.ac.uk/wiki/Software#SAP +Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/sap/trunk/ +Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/sap/trunk/ + +Package: sap +Architecture: any +Depends: ${shlibs:Depends}, ${misc:Depends} +Enhances: t-coffee +Description: Pairwise protein structure alignment via double dynamic programming + In contrast to DNA, proteins exhibit an apparently unlimited variety of + structure. This is a necessary requirement of the vast array of + differing functions that they perform in the maintainance of life, + again, in contrast to the relatively static archival function of DNA. + Not only do we observe a bewildering variety of form but even within a + common structure, there is variation in the lengths and orientation + substructures. Such variation is both a reflection on the very long time + periods over which some structures have diverged and also a consequence + of the fact that proteins cannot be completely rigid bodies but must + have flexibility to accommodate the structural changes that are almost + always necessary for them to perform their functions. These aspects make + comparing structure and finding structural similarity over long + divergence times very difficult. Indeed, computationally, the problem of + recognizing similarity is one of three-dimensional pattern recognition, + which is a notoriously difficult problem for computers to perform. In + this chapter, guidance is provided on the use of a flexible structure + comparison method that overcomes many of the problems of comparing + protein structures that may exhibit only weak similarity. + diff --git a/debian/copyright b/debian/copyright new file mode 100644 index 0000000..83d9ee2 --- /dev/null +++ b/debian/copyright @@ -0,0 +1,10 @@ +Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Source: http://mathbio.nimr.mrc.ac.uk/download/SAP/sap-1.1.1.tar.gz + +Files: * +Copyright: © 2008-2010 Willie Taylor <[email protected]> +License: GPL-v3 + +Files: debian/* +Copyright: © 2012 Andreas Tille <[email protected]> +License: GPL-v3 diff --git a/debian/rules b/debian/rules new file mode 100755 index 0000000..6055261 --- /dev/null +++ b/debian/rules @@ -0,0 +1,6 @@ +#!/usr/bin/make -f + +# DH_VERBOSE := 1 + +%: + dh $@ diff --git a/debian/upstream b/debian/upstream new file mode 100644 index 0000000..98a61ea --- /dev/null +++ b/debian/upstream @@ -0,0 +1,20 @@ +Reference: + - Author: William R. Taylor + Title: Protein Structure Comparison Using SAP + Booktitle: "Protein Structure Prediction: Methods and Protocols" + Year: 2000 + Volume: 143 + Pages: 19-32 + DOI: 10.1385/1-59259-368-2:19 + URL: http://www.springerprotocols.com/Abstract/doi/10.1385/1-59259-368-2:19 + - Author: William R. Taylor + Title: Protein structure comparison using iterated double dynamic programming + Journal: Protein Science + Year: 1999 + Volume: 8 + Number: 3 + Pages: 654-65 + DOI: 10.1110/ps.8.3.654 + PMID: 10091668 + URL: http://onlinelibrary.wiley.com/doi/10.1110/ps.8.3.654/abstract + eprint: http://onlinelibrary.wiley.com/doi/10.1110/ps.8.3.654/pdf -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/sap.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
