[med-svn] r14778 - in trunk/packages/rostlab/rate4site/trunk: . debian
Guy Yachdav
gyachdav-guest at alioth.debian.org
Tue Oct 1 17:22:26 UTC 2013
Author: gyachdav-guest
Date: 2013-10-01 17:22:25 +0000 (Tue, 01 Oct 2013)
New Revision: 14778
Added:
trunk/packages/rostlab/rate4site/trunk/debian/
trunk/packages/rostlab/rate4site/trunk/debian/changelog
trunk/packages/rostlab/rate4site/trunk/debian/compat
trunk/packages/rostlab/rate4site/trunk/debian/control
trunk/packages/rostlab/rate4site/trunk/debian/copyright
trunk/packages/rostlab/rate4site/trunk/debian/files
trunk/packages/rostlab/rate4site/trunk/debian/rate4site.substvars
trunk/packages/rostlab/rate4site/trunk/debian/rules
trunk/packages/rostlab/rate4site/trunk/debian/source/
trunk/packages/rostlab/rate4site/trunk/debian/upstream
trunk/packages/rostlab/rate4site/trunk/debian/watch
Removed:
trunk/packages/rostlab/rate4site/trunk/changelog
trunk/packages/rostlab/rate4site/trunk/compat
trunk/packages/rostlab/rate4site/trunk/control
trunk/packages/rostlab/rate4site/trunk/copyright
trunk/packages/rostlab/rate4site/trunk/files
trunk/packages/rostlab/rate4site/trunk/rate4site.substvars
trunk/packages/rostlab/rate4site/trunk/rules
trunk/packages/rostlab/rate4site/trunk/source/
trunk/packages/rostlab/rate4site/trunk/upstream
trunk/packages/rostlab/rate4site/trunk/watch
Log:
reorgnized debian folder
Deleted: trunk/packages/rostlab/rate4site/trunk/changelog
===================================================================
--- trunk/packages/rostlab/rate4site/trunk/changelog 2013-10-01 17:18:44 UTC (rev 14777)
+++ trunk/packages/rostlab/rate4site/trunk/changelog 2013-10-01 17:22:25 UTC (rev 14778)
@@ -1,5 +0,0 @@
-rate4site (3.0.0-1) UNRELEASED; urgency=low
-
- * Initial release.
-
- -- Guy Yachdav <gyachdav at rostlab.org> Mon, 05 Aug 2013 21:06:00 +0200
Deleted: trunk/packages/rostlab/rate4site/trunk/compat
===================================================================
--- trunk/packages/rostlab/rate4site/trunk/compat 2013-10-01 17:18:44 UTC (rev 14777)
+++ trunk/packages/rostlab/rate4site/trunk/compat 2013-10-01 17:22:25 UTC (rev 14778)
@@ -1 +0,0 @@
-8
Deleted: trunk/packages/rostlab/rate4site/trunk/control
===================================================================
--- trunk/packages/rostlab/rate4site/trunk/control 2013-10-01 17:18:44 UTC (rev 14777)
+++ trunk/packages/rostlab/rate4site/trunk/control 2013-10-01 17:22:25 UTC (rev 14778)
@@ -1,21 +0,0 @@
-Source: rate4site
-Section: science
-Priority: extra
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Guy Yachdav <gyachdav at rostlab.org>, Laszlo Kajan <lkajan at rostlab.org>
-Build-Depends: debhelper (>= 9.0.0), autotools-dev
-Standards-Version: 3.9.4
-Homepage: http://www.tau.ac.il/~itaymay/cp/rate4site.html
-Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/rostlab/rate4site
-Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/rostlab/rate4site
-
-
-Package: rate4site
-Architecture: all
-Pre-Depends: debconf (>= 0.5)
-Description: detection of conserved amino-acid sites
- The rate of evolution is not constant among amino acid sites: some positions evolve slowly and are commonly referred to as "conserved", while others evolve rapidly and are referred to as "variable". The rate variations correspond to different levels of purifying selection acting on these sites. The purifying selection can be the result of geometrical constraints on the folding of the protein into its 3D structure, constraints at amino acid sites involved in enzymatic activity or in ligand binding or, alternatively, at amino acid sites that take part in protein-protein interactions. Rate4Site calculates the relative evolutionary rate at each site using a probabilistic-based evolutionary model. This allows taking into account the stochastic process underlying sequence evolution within protein families and the phylogenetic tree of the proteins in the family. The conservation score at a site corresponds to the site's evolutionary rate.
- .
- Methodology:
- The sole obligatory input to Rate4Site is an MSA file. The program then computes a phylogenetic tree that is consistent with the available MSA (the user can also input a pre-calculated tree). It then calculates the relative conservation score for each site in the MSA. This is carried out using either an empirical Bayesian method or a maximum likelihood method (Pupko et al., 2002). The differences between the two methods are explained in details in Mayrose et al (2004).
-
Deleted: trunk/packages/rostlab/rate4site/trunk/copyright
===================================================================
--- trunk/packages/rostlab/rate4site/trunk/copyright 2013-10-01 17:18:44 UTC (rev 14777)
+++ trunk/packages/rostlab/rate4site/trunk/copyright 2013-10-01 17:22:25 UTC (rev 14778)
@@ -1,29 +0,0 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
-Upstream-Name: predictprotein
-Upstream-Contact: Guy Yachdav <gyachdav at rostlab.org>
-Source: ftp://rostlab.org/rate4site/
-
-Files: debian/*
-Copyright: 2013 Guy Yachdav <gyachdav at rostlab.org>
-License: GPL-3+
-
-Files: *
-Copyright: 2013 Nir Ben-Tal
-License: GPL-3+
-
-License: GPL-3+
- This program is free software: you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation, either version 3 of the License, or
- (at your option) any later version.
- .
- This program is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
- .
- You should have received a copy of the GNU General Public License
- along with this program. If not, see <http://www.gnu.org/licenses/>.
- .
- On Debian systems, the complete text of the GNU General Public
- License version 3 can be found in "/usr/share/common-licenses/GPL-3".
Copied: trunk/packages/rostlab/rate4site/trunk/debian/changelog (from rev 14777, trunk/packages/rostlab/rate4site/trunk/changelog)
===================================================================
--- trunk/packages/rostlab/rate4site/trunk/debian/changelog (rev 0)
+++ trunk/packages/rostlab/rate4site/trunk/debian/changelog 2013-10-01 17:22:25 UTC (rev 14778)
@@ -0,0 +1,5 @@
+rate4site (3.0.0-1) UNRELEASED; urgency=low
+
+ * Initial release.
+
+ -- Guy Yachdav <gyachdav at rostlab.org> Mon, 05 Aug 2013 21:06:00 +0200
Copied: trunk/packages/rostlab/rate4site/trunk/debian/compat (from rev 14777, trunk/packages/rostlab/rate4site/trunk/compat)
===================================================================
--- trunk/packages/rostlab/rate4site/trunk/debian/compat (rev 0)
+++ trunk/packages/rostlab/rate4site/trunk/debian/compat 2013-10-01 17:22:25 UTC (rev 14778)
@@ -0,0 +1 @@
+8
Copied: trunk/packages/rostlab/rate4site/trunk/debian/control (from rev 14777, trunk/packages/rostlab/rate4site/trunk/control)
===================================================================
--- trunk/packages/rostlab/rate4site/trunk/debian/control (rev 0)
+++ trunk/packages/rostlab/rate4site/trunk/debian/control 2013-10-01 17:22:25 UTC (rev 14778)
@@ -0,0 +1,21 @@
+Source: rate4site
+Section: science
+Priority: extra
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Guy Yachdav <gyachdav at rostlab.org>, Laszlo Kajan <lkajan at rostlab.org>
+Build-Depends: debhelper (>= 9.0.0), autotools-dev
+Standards-Version: 3.9.4
+Homepage: http://www.tau.ac.il/~itaymay/cp/rate4site.html
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/rostlab/rate4site
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/rostlab/rate4site
+
+
+Package: rate4site
+Architecture: all
+Pre-Depends: debconf (>= 0.5)
+Description: detection of conserved amino-acid sites
+ The rate of evolution is not constant among amino acid sites: some positions evolve slowly and are commonly referred to as "conserved", while others evolve rapidly and are referred to as "variable". The rate variations correspond to different levels of purifying selection acting on these sites. The purifying selection can be the result of geometrical constraints on the folding of the protein into its 3D structure, constraints at amino acid sites involved in enzymatic activity or in ligand binding or, alternatively, at amino acid sites that take part in protein-protein interactions. Rate4Site calculates the relative evolutionary rate at each site using a probabilistic-based evolutionary model. This allows taking into account the stochastic process underlying sequence evolution within protein families and the phylogenetic tree of the proteins in the family. The conservation score at a site corresponds to the site's evolutionary rate.
+ .
+ Methodology:
+ The sole obligatory input to Rate4Site is an MSA file. The program then computes a phylogenetic tree that is consistent with the available MSA (the user can also input a pre-calculated tree). It then calculates the relative conservation score for each site in the MSA. This is carried out using either an empirical Bayesian method or a maximum likelihood method (Pupko et al., 2002). The differences between the two methods are explained in details in Mayrose et al (2004).
+
Copied: trunk/packages/rostlab/rate4site/trunk/debian/copyright (from rev 14777, trunk/packages/rostlab/rate4site/trunk/copyright)
===================================================================
--- trunk/packages/rostlab/rate4site/trunk/debian/copyright (rev 0)
+++ trunk/packages/rostlab/rate4site/trunk/debian/copyright 2013-10-01 17:22:25 UTC (rev 14778)
@@ -0,0 +1,29 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: predictprotein
+Upstream-Contact: Guy Yachdav <gyachdav at rostlab.org>
+Source: ftp://rostlab.org/rate4site/
+
+Files: debian/*
+Copyright: 2013 Guy Yachdav <gyachdav at rostlab.org>
+License: GPL-3+
+
+Files: *
+Copyright: 2013 Nir Ben-Tal
+License: GPL-3+
+
+License: GPL-3+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+ .
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+ .
+ On Debian systems, the complete text of the GNU General Public
+ License version 3 can be found in "/usr/share/common-licenses/GPL-3".
Copied: trunk/packages/rostlab/rate4site/trunk/debian/files (from rev 14777, trunk/packages/rostlab/rate4site/trunk/files)
===================================================================
--- trunk/packages/rostlab/rate4site/trunk/debian/files (rev 0)
+++ trunk/packages/rostlab/rate4site/trunk/debian/files 2013-10-01 17:22:25 UTC (rev 14778)
@@ -0,0 +1 @@
+rate4site_3.0.0-1_all.deb science extra
Copied: trunk/packages/rostlab/rate4site/trunk/debian/rate4site.substvars (from rev 14777, trunk/packages/rostlab/rate4site/trunk/rate4site.substvars)
===================================================================
--- trunk/packages/rostlab/rate4site/trunk/debian/rate4site.substvars (rev 0)
+++ trunk/packages/rostlab/rate4site/trunk/debian/rate4site.substvars 2013-10-01 17:22:25 UTC (rev 14778)
@@ -0,0 +1 @@
+misc:Depends=
Copied: trunk/packages/rostlab/rate4site/trunk/debian/rules (from rev 14777, trunk/packages/rostlab/rate4site/trunk/rules)
===================================================================
--- trunk/packages/rostlab/rate4site/trunk/debian/rules (rev 0)
+++ trunk/packages/rostlab/rate4site/trunk/debian/rules 2013-10-01 17:22:25 UTC (rev 14778)
@@ -0,0 +1,9 @@
+#!/usr/bin/make -f
+#export DH_VERBOSE=1
+
+%:
+ dh $@
+
+get-orig-source:
+ mkdir -p ../tarballs
+ uscan --verbose --force-download --destdir=../tarballs
Copied: trunk/packages/rostlab/rate4site/trunk/debian/upstream (from rev 14777, trunk/packages/rostlab/rate4site/trunk/upstream)
===================================================================
--- trunk/packages/rostlab/rate4site/trunk/debian/upstream (rev 0)
+++ trunk/packages/rostlab/rate4site/trunk/debian/upstream 2013-10-01 17:22:25 UTC (rev 14778)
@@ -0,0 +1,14 @@
+Bug-Database: https://rostlab.org/bugzilla3/buglist.cgi?product=rate4site/&component=rate4site/&resolution=---
+Bug-Submit: https://rostlab.org/bugzilla3/enter_bug.cgi?product=rate4site/
+Reference:
+ Author: Mayrose, I., Graur, D., Ben-Tal, N., and Pupko, T.
+ Title: Comparison of site-specific rate-inference methods: Bayesian methods are superior.
+ Journal: Mol Biol Evol
+ Year: 2004
+ Volume: 21
+ Number: 2
+ Pages: 1781-1791
+ DOI: 10.1093/molbev/msh194
+ PMID: 15201400
+ URL: http://mbe.oxfordjournals.org/content/21/9/1781.abstract
+ eprint: http://mbe.oxfordjournals.org/content/21/9/1781.full
Copied: trunk/packages/rostlab/rate4site/trunk/debian/watch (from rev 14777, trunk/packages/rostlab/rate4site/trunk/watch)
===================================================================
--- trunk/packages/rostlab/rate4site/trunk/debian/watch (rev 0)
+++ trunk/packages/rostlab/rate4site/trunk/debian/watch 2013-10-01 17:22:25 UTC (rev 14778)
@@ -0,0 +1,2 @@
+version=3
+opts=pasv ftp://rostlab.org/rate4site//rate4site-([0-9.]+)\.tar\.gz debian update
Deleted: trunk/packages/rostlab/rate4site/trunk/files
===================================================================
--- trunk/packages/rostlab/rate4site/trunk/files 2013-10-01 17:18:44 UTC (rev 14777)
+++ trunk/packages/rostlab/rate4site/trunk/files 2013-10-01 17:22:25 UTC (rev 14778)
@@ -1 +0,0 @@
-rate4site_3.0.0-1_all.deb science extra
Deleted: trunk/packages/rostlab/rate4site/trunk/rate4site.substvars
===================================================================
--- trunk/packages/rostlab/rate4site/trunk/rate4site.substvars 2013-10-01 17:18:44 UTC (rev 14777)
+++ trunk/packages/rostlab/rate4site/trunk/rate4site.substvars 2013-10-01 17:22:25 UTC (rev 14778)
@@ -1 +0,0 @@
-misc:Depends=
Deleted: trunk/packages/rostlab/rate4site/trunk/rules
===================================================================
--- trunk/packages/rostlab/rate4site/trunk/rules 2013-10-01 17:18:44 UTC (rev 14777)
+++ trunk/packages/rostlab/rate4site/trunk/rules 2013-10-01 17:22:25 UTC (rev 14778)
@@ -1,9 +0,0 @@
-#!/usr/bin/make -f
-#export DH_VERBOSE=1
-
-%:
- dh $@
-
-get-orig-source:
- mkdir -p ../tarballs
- uscan --verbose --force-download --destdir=../tarballs
Deleted: trunk/packages/rostlab/rate4site/trunk/upstream
===================================================================
--- trunk/packages/rostlab/rate4site/trunk/upstream 2013-10-01 17:18:44 UTC (rev 14777)
+++ trunk/packages/rostlab/rate4site/trunk/upstream 2013-10-01 17:22:25 UTC (rev 14778)
@@ -1,14 +0,0 @@
-Bug-Database: https://rostlab.org/bugzilla3/buglist.cgi?product=rate4site/&component=rate4site/&resolution=---
-Bug-Submit: https://rostlab.org/bugzilla3/enter_bug.cgi?product=rate4site/
-Reference:
- Author: Mayrose, I., Graur, D., Ben-Tal, N., and Pupko, T.
- Title: Comparison of site-specific rate-inference methods: Bayesian methods are superior.
- Journal: Mol Biol Evol
- Year: 2004
- Volume: 21
- Number: 2
- Pages: 1781-1791
- DOI: 10.1093/molbev/msh194
- PMID: 15201400
- URL: http://mbe.oxfordjournals.org/content/21/9/1781.abstract
- eprint: http://mbe.oxfordjournals.org/content/21/9/1781.full
Deleted: trunk/packages/rostlab/rate4site/trunk/watch
===================================================================
--- trunk/packages/rostlab/rate4site/trunk/watch 2013-10-01 17:18:44 UTC (rev 14777)
+++ trunk/packages/rostlab/rate4site/trunk/watch 2013-10-01 17:22:25 UTC (rev 14778)
@@ -1,2 +0,0 @@
-version=3
-opts=pasv ftp://rostlab.org/rate4site//rate4site-([0-9.]+)\.tar\.gz debian update
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