[med-svn] r11696 - in trunk/packages/profbval: . trunk trunk/debian trunk/debian/source
Christof Anger
freeyourmind-guest at alioth.debian.org
Tue Jul 10 14:17:52 UTC 2012
Author: freeyourmind-guest
Date: 2012-07-10 14:17:52 +0000 (Tue, 10 Jul 2012)
New Revision: 11696
Added:
trunk/packages/profbval/trunk/debian/
trunk/packages/profbval/trunk/debian/changelog
trunk/packages/profbval/trunk/debian/compat
trunk/packages/profbval/trunk/debian/control
trunk/packages/profbval/trunk/debian/copyright
trunk/packages/profbval/trunk/debian/docs
trunk/packages/profbval/trunk/debian/rules
trunk/packages/profbval/trunk/debian/source/
trunk/packages/profbval/trunk/debian/source/format
trunk/packages/profbval/trunk/debian/upstream
trunk/packages/profbval/trunk/debian/watch
Modified:
trunk/packages/profbval/
Log:
Minor changes
Property changes on: trunk/packages/profbval
___________________________________________________________________
Added: svn:ignore
+ build-area
Property changes on: trunk/packages/profbval/trunk/debian
___________________________________________________________________
Added: mergeWithUpstream
+ 1
Added: trunk/packages/profbval/trunk/debian/changelog
===================================================================
--- trunk/packages/profbval/trunk/debian/changelog (rev 0)
+++ trunk/packages/profbval/trunk/debian/changelog 2012-07-10 14:17:52 UTC (rev 11696)
@@ -0,0 +1,98 @@
+profbval (1.0.18) unstable; urgency=low
+ * GPL license
+ -- Laszlo Kajan <lkajan at rostlab.org> Mon, 10 July 2012 13:20:18 +0200
+
+profbval (1.0.16) unstable; urgency=low
+
+ * man page update for multiple output files and formats
+ * moved references to PP standard section
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Mon, 16 May 2011 13:37:18 +0200
+
+profbval (1.0.15) unstable; urgency=low
+
+ * Added ability to create multiple outputs with the intention to save
+ output in multiple formats
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Wed, 11 May 2011 15:39:45 +0200
+
+profbval (1.0.14) stable; urgency=low
+
+ * Made prof output regexp line recognize more prof outputs
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Wed, 12 Jan 2011 17:41:42 +0100
+
+profbval (1.0.13)
+
+ * Input sequence now converted to upper case before processing (and so lower case sequences are now accepted)
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Mon, 20 Sep 2010 17:19:10 +0200
+
+profbval (1.0.12)
+
+ * Now accepts `O' as a valid amino acid (for pyrrolysine)
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Wed, 30 Jun 2010 11:07:23 +0200
+
+profbval (1.0.11)
+
+ * Now accepts `U' as a valid amino acid (for selenocysteine)
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Tue, 29 Jun 2010 11:24:37 +0200
+
+profbval (1.0.10)
+
+ * Documented mode 5 a bit on the man page
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Tue, 22 Jun 2010 12:44:59 +0200
+
+profbval (1.0.9)
+
+ * Made profbval completely silent when debug is off and operation is normal
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Wed, 16 Jun 2010 11:48:10 +0200
+
+profbval (1.0.8)
+
+ * -> automake/autoconf
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Mon, 14 Jun 2010 12:15:19 +0200
+
+profbval (1.0.7)
+
+ * Added early checking of input fasta sequence for valid sequence
+ * Added debug command line option
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Mon, 03 May 2010 14:39:22 +0200
+
+profbval (1.0.6)
+
+ * Documented environment variable PROFBVAL_ROOT
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Sat, 19 Dec 2009 11:27:53 +0100
+
+profbval (1.0.5)
+
+ * snapfun(snap) output mode added
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Fri, 11 Dec 2009 22:56:36 +0100
+
+profbval (1.0.4)
+
+ * temporary directory collision problem solved
+ * prefix is now correctly respected
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Fri, 11 Dec 2009 14:02:57 +0100
+
+profbval (1.0.2)
+
+ * Examples added.
+
+ -- Guy Yachdav <gyahcdav at rostlab.org> Wed, 09 Dec 2009 15:51:56 +0100
+
+profbval (1.0.0)
+
+ * Initial version.
+
+ -- Guy Yachdav <gyahcdav at rostlab.org> Tue, 01 Dec 2009 12:51:59 +0200
+
Added: trunk/packages/profbval/trunk/debian/compat
===================================================================
--- trunk/packages/profbval/trunk/debian/compat (rev 0)
+++ trunk/packages/profbval/trunk/debian/compat 2012-07-10 14:17:52 UTC (rev 11696)
@@ -0,0 +1 @@
+8
Added: trunk/packages/profbval/trunk/debian/control
===================================================================
--- trunk/packages/profbval/trunk/debian/control (rev 0)
+++ trunk/packages/profbval/trunk/debian/control 2012-07-10 14:17:52 UTC (rev 11696)
@@ -0,0 +1,15 @@
+Source: profbval
+Section: science
+Priority: extra
+Maintainer: Guy Yachdav <gyachdav at rostlab.org>
+Uploaders: Laszlo Kajan <lkajan at rostlab.org>
+Build-Depends: debhelper (>= 8), perl
+Standards-Version: 3.9.3
+Homepage: http://www.predictprotein.org/docs.php
+
+Package: profbval
+Architecture: all
+Depends: ${perl:Depends}, ${shlibs:Depends}, ${misc:Depends}, debconf (>= 0.5), profnet-bval
+Recommends: profphd
+Description: predicts flexibile/rigid residues from sequence
+ PROFBval predicts bvalue - rigid and flexible residues.
Added: trunk/packages/profbval/trunk/debian/copyright
===================================================================
--- trunk/packages/profbval/trunk/debian/copyright (rev 0)
+++ trunk/packages/profbval/trunk/debian/copyright 2012-07-10 14:17:52 UTC (rev 11696)
@@ -0,0 +1,690 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: profbval
+Upstream-Contact: A. Schlessinger <avnersch at gmail.com>
+Source: ftp://rostlab.org/profbval/
+
+Files: *
+Authors:
+
+ B. <rost at in.tum.de>
+ A. Schlessinger <avnersch at gmail.com>
+
+Copyright:
+
+ Copyright © 212 Burkhard Rost <rost at rostlab.org>
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+
+ You may not impose any further restrictions on the exercise of the
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+any patent claim is infringed by making, using, selling, offering for
+sale, or importing the Program or any portion of it.
+
+ 11. Patents.
+
+ A "contributor" is a copyright holder who authorizes use under this
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+ A contributor's "essential patent claims" are all patent claims
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+covered work in a country, or your recipient's use of the covered work
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+
+ If, pursuant to or in connection with a single transaction or
+arrangement, you convey, or propagate by procuring conveyance of, a
+covered work, and grant a patent license to some of the parties
+receiving the covered work authorizing them to use, propagate, modify
+or convey a specific copy of the covered work, then the patent license
+you grant is automatically extended to all recipients of the covered
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+
+ A patent license is "discriminatory" if it does not include within
+the scope of its coverage, prohibits the exercise of, or is
+conditioned on the non-exercise of one or more of the rights that are
+specifically granted under this License. You may not convey a covered
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+for and in connection with specific products or compilations that
+contain the covered work, unless you entered into that arrangement,
+or that patent license was granted, prior to 28 March 2007.
+
+ Nothing in this License shall be construed as excluding or limiting
+any implied license or other defenses to infringement that may
+otherwise be available to you under applicable patent law.
+
+ 12. No Surrender of Others' Freedom.
+
+ If conditions are imposed on you (whether by court order, agreement or
+otherwise) that contradict the conditions of this License, they do not
+excuse you from the conditions of this License. If you cannot convey a
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+not convey it at all. For example, if you agree to terms that obligate you
+to collect a royalty for further conveying from those to whom you convey
+the Program, the only way you could satisfy both those terms and this
+License would be to refrain entirely from conveying the Program.
+
+ 13. Use with the GNU Affero General Public License.
+
+ Notwithstanding any other provision of this License, you have
+permission to link or combine any covered work with a work licensed
+under version 3 of the GNU Affero General Public License into a single
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+License will continue to apply to the part which is the covered work,
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+combination as such.
+
+ 14. Revised Versions of this License.
+
+ The Free Software Foundation may publish revised and/or new versions of
+the GNU General Public License from time to time. Such new versions will
+be similar in spirit to the present version, but may differ in detail to
+address new problems or concerns.
+
+ Each version is given a distinguishing version number. If the
+Program specifies that a certain numbered version of the GNU General
+Public License "or any later version" applies to it, you have the
+option of following the terms and conditions either of that numbered
+version or of any later version published by the Free Software
+Foundation. If the Program does not specify a version number of the
+GNU General Public License, you may choose any version ever published
+by the Free Software Foundation.
+
+ If the Program specifies that a proxy can decide which future
+versions of the GNU General Public License can be used, that proxy's
+public statement of acceptance of a version permanently authorizes you
+to choose that version for the Program.
+
+ Later license versions may give you additional or different
+permissions. However, no additional obligations are imposed on any
+author or copyright holder as a result of your choosing to follow a
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+
+ 15. Disclaimer of Warranty.
+
+ THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
+APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
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+ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
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+ 17. Interpretation of Sections 15 and 16.
+
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+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+ END OF TERMS AND CONDITIONS
+
+ How to Apply These Terms to Your New Programs
+
+ If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+ To do so, attach the following notices to the program. It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+ <one line to give the program's name and a brief idea of what it does.>
+ Copyright (C) <year> <name of author>
+
+ 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/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+ If the program does terminal interaction, make it output a short
+notice like this when it starts in an interactive mode:
+
+ <program> Copyright (C) <year> <name of author>
+ This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+ This is free software, and you are welcome to redistribute it
+ under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License. Of course, your program's commands
+might be different; for a GUI interface, you would use an "about box".
+
+ You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU GPL, see
+<http://www.gnu.org/licenses/>.
+
+ The GNU General Public License does not permit incorporating your program
+into proprietary programs. If your program is a subroutine library, you
+may consider it more useful to permit linking proprietary applications with
+the library. If this is what you want to do, use the GNU Lesser General
+Public License instead of this License. But first, please read
+<http://www.gnu.org/philosophy/why-not-lgpl.html>.
Added: trunk/packages/profbval/trunk/debian/docs
===================================================================
--- trunk/packages/profbval/trunk/debian/docs (rev 0)
+++ trunk/packages/profbval/trunk/debian/docs 2012-07-10 14:17:52 UTC (rev 11696)
@@ -0,0 +1 @@
+
Added: trunk/packages/profbval/trunk/debian/rules
===================================================================
--- trunk/packages/profbval/trunk/debian/rules (rev 0)
+++ trunk/packages/profbval/trunk/debian/rules 2012-07-10 14:17:52 UTC (rev 11696)
@@ -0,0 +1,105 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+# Sample debian/rules that uses debhelper.
+# This file was originally written by Joey Hess and Craig Small.
+# As a special exception, when this file is copied by dh-make into a
+# dh-make output file, you may use that output file without restriction.
+# This special exception was added by Craig Small in version 0.37 of dh-make.
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+
+# These are used for cross-compiling and for saving the configure script
+# from having to guess our platform (since we know it already)
+DEB_HOST_GNU_TYPE ?= $(shell dpkg-architecture -qDEB_HOST_GNU_TYPE)
+DEB_BUILD_GNU_TYPE ?= $(shell dpkg-architecture -qDEB_BUILD_GNU_TYPE)
+ifneq ($(DEB_HOST_GNU_TYPE),$(DEB_BUILD_GNU_TYPE))
+CROSS= --build $(DEB_BUILD_GNU_TYPE) --host $(DEB_HOST_GNU_TYPE)
+else
+CROSS= --build $(DEB_BUILD_GNU_TYPE)
+endif
+
+
+
+config.status: configure
+ dh_testdir
+ # Add here commands to configure the package.
+ifneq "$(wildcard /usr/share/misc/config.sub)" ""
+ cp -f /usr/share/misc/config.sub config.sub
+endif
+ifneq "$(wildcard /usr/share/misc/config.guess)" ""
+ cp -f /usr/share/misc/config.guess config.guess
+endif
+ ./configure $(CROSS) --prefix=/usr --mandir=\$${prefix}/share/man --infodir=\$${prefix}/share/info CFLAGS="$(CFLAGS)" LDFLAGS="-Wl,-z,defs" --sysconfdir=/etc
+
+
+build: build-stamp
+
+build-stamp: config.status
+ dh_testdir
+
+ # Add here commands to compile the package.
+ $(MAKE)
+ #docbook-to-man debian/profbval.sgml > profbval.1
+
+ touch $@
+
+clean:
+ dh_testdir
+ dh_testroot
+ rm -f build-stamp
+
+ # Add here commands to clean up after the build process.
+ [ ! -f Makefile ] || $(MAKE) distclean
+ rm -f config.sub config.guess
+
+ dh_clean
+
+install: build
+ dh_testdir
+ dh_testroot
+ dh_prep
+ dh_installdirs
+
+ # Add here commands to install the package into debian/profbval.
+ $(MAKE) DESTDIR=$(CURDIR)/debian/profbval install
+
+
+# Build architecture-independent files here.
+binary-indep: build install
+ dh_testdir
+ dh_testroot
+ dh_installchangelogs ChangeLog
+ dh_installdocs
+ dh_installexamples
+# dh_install
+# dh_installmenu
+# dh_installdebconf
+# dh_installlogrotate
+# dh_installemacsen
+# dh_installpam
+# dh_installmime
+# dh_python
+# dh_installinit
+# dh_installcron
+# dh_installinfo
+ dh_installman
+ dh_link
+ dh_strip
+ dh_compress
+ dh_fixperms
+# dh_perl
+# dh_makeshlibs
+ dh_installdeb
+ dh_shlibdeps
+ dh_gencontrol
+ dh_md5sums
+ dh_builddeb
+
+# Build architecture-dependent files here.
+binary-arch: build install
+# We have nothing to do by default.
+
+binary: binary-indep binary-arch
+.PHONY: build clean binary-indep binary-arch binary install
Property changes on: trunk/packages/profbval/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/profbval/trunk/debian/source/format
===================================================================
--- trunk/packages/profbval/trunk/debian/source/format (rev 0)
+++ trunk/packages/profbval/trunk/debian/source/format 2012-07-10 14:17:52 UTC (rev 11696)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/profbval/trunk/debian/upstream
===================================================================
--- trunk/packages/profbval/trunk/debian/upstream (rev 0)
+++ trunk/packages/profbval/trunk/debian/upstream 2012-07-10 14:17:52 UTC (rev 11696)
@@ -0,0 +1,20 @@
+Name: profbval
+Reference:
+- Author: Schlessinger A, Rost B.
+ Title: 'Protein flexibility and rigidity predicted from sequence.'
+ Journal: Proteins
+ Year: 2005
+ Volume: 61
+ Number: 1
+ Pages: 115-26
+ URL: http://www.ncbi.nlm.nih.gov/pubmed/16080156
+ PMID: 16080156
+- Author: Schlessinger A, Yachdav G, & Rost B.
+ Title: 'PROFbval: predict flexible and rigid residues in proteins.'
+ Journal: Bioinformatics
+ Year: 2006
+ Volume: 22
+ Number: 7
+ Pages: 891-3
+ URL: http://www.ncbi.nlm.nih.gov/pubmed?term=PROFbval%3A%20predict%20flexible%20and%20rigid%20residues%20in%20proteins
+ PMID: 16455751
Added: trunk/packages/profbval/trunk/debian/watch
===================================================================
--- trunk/packages/profbval/trunk/debian/watch (rev 0)
+++ trunk/packages/profbval/trunk/debian/watch 2012-07-10 14:17:52 UTC (rev 11696)
@@ -0,0 +1,2 @@
+version=3
+opts=pasv ftp://rostlab.org/profbval/profbval-([0-9.]+)\.tar\.gz
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