[med-svn] r7956 - in trunk/packages/rostlab/profphd/trunk: . debian debian/source
Laszlo Kajan
lkajan-guest at alioth.debian.org
Tue Sep 27 15:29:37 UTC 2011
Author: lkajan-guest
Date: 2011-09-27 15:29:37 +0000 (Tue, 27 Sep 2011)
New Revision: 7956
Added:
trunk/packages/rostlab/profphd/trunk/debian/
trunk/packages/rostlab/profphd/trunk/debian/README.Debian
trunk/packages/rostlab/profphd/trunk/debian/changelog
trunk/packages/rostlab/profphd/trunk/debian/compat
trunk/packages/rostlab/profphd/trunk/debian/control
trunk/packages/rostlab/profphd/trunk/debian/copyright
trunk/packages/rostlab/profphd/trunk/debian/patches/
trunk/packages/rostlab/profphd/trunk/debian/profphd.install
trunk/packages/rostlab/profphd/trunk/debian/rules
trunk/packages/rostlab/profphd/trunk/debian/source/
trunk/packages/rostlab/profphd/trunk/debian/source/format
trunk/packages/rostlab/profphd/trunk/debian/upstream-metadata.yaml
trunk/packages/rostlab/profphd/trunk/debian/watch
Log:
profphd - secondary structure, accessibility and transmembrane helix predictor from Burkhard Rost, version 1.0.35 is ready for upload; lintian does not complain
Property changes on: trunk/packages/rostlab/profphd/trunk/debian
___________________________________________________________________
Added: mergeWithUpstream
+ 1
Added: trunk/packages/rostlab/profphd/trunk/debian/README.Debian
===================================================================
--- trunk/packages/rostlab/profphd/trunk/debian/README.Debian (rev 0)
+++ trunk/packages/rostlab/profphd/trunk/debian/README.Debian 2011-09-27 15:29:37 UTC (rev 7956)
@@ -0,0 +1,11 @@
+profphd for Debian
+------------------
+
+References
+==========
+
+* Rost, B. and Sander, C. (1994a). Combining evolutionary information and neural networks to predict protein secondary structure. Proteins, 19(1), 55-72.
+* Rost, B. and Sander, C. (1994b). Conservation and prediction of solvent accessibility in protein families. Proteins, 20(3), 216-26.
+* Rost, B., Casadio, R., Fariselli, P., and Sander, C. (1995). Transmembrane helices predicted at 95% accuracy. Protein Sci, 4(3), 521-33.
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Tue, 17 Nov 2009 10:50:19 +0100
Added: trunk/packages/rostlab/profphd/trunk/debian/changelog
===================================================================
--- trunk/packages/rostlab/profphd/trunk/debian/changelog (rev 0)
+++ trunk/packages/rostlab/profphd/trunk/debian/changelog 2011-09-27 15:29:37 UTC (rev 7956)
@@ -0,0 +1,224 @@
+profphd (1.0.35-1) UNRELEASED; urgency=low
+
+ * new upstream release
+ * added Replaces and Conflicts to control file for
+ profphd-perl and profphd-data
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Tue, 27 Sep 2011 11:05:27 +0200
+
+profphd (1.0.34) unstable; urgency=low
+
+ * fixed "HTMTOP_RID :-10.942" bug in src/prof/scr/lib/lib-prof.pl
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Fri, 20 May 2011 21:09:41 +0200
+
+profphd (1.0.33) unstable; urgency=low
+
+ * use warnings in phd.pl
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Tue, 01 Mar 2011 16:00:23 +0100
+
+profphd (1.0.32) unstable; urgency=low
+
+ * copyright corrected to GPL
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Fri, 26 Nov 2010 16:49:36 +0100
+
+profphd (1.0.31) unstable; urgency=low
+
+ * Makefile update - works now on Ubuntu as well (/bin/sh bug)
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Fri, 26 Nov 2010 16:49:36 +0100
+
+profphd (1.0.29)
+
+ * [A-Z.~_!] in src/prof/scr/lib/lib-col.pl
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Wed, 20 Oct 2010 14:28:49 +0200
+
+profphd (1.0.28)
+
+ * provide NORM_EXP for Selenocysteine:
+ $NORM_EXP{"U"} = $NORM_EXP{"C"}; # U - Selenocysteine # lkajan quick hack
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Wed, 20 Oct 2010 13:54:03 +0200
+
+profphd (1.0.27)
+
+ * fasta AA pattern now [A-Z.~_!]
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Wed, 20 Oct 2010 11:54:27 +0200
+
+profphd (1.0.26)
+
+ * Documented `optJury'
+ * prof in debug mode now dumps final parameter values before starting actual work
+ * Proper error reporting when input file is empty
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Thu, 07 Oct 2010 08:48:44 +0200
+
+profphd (1.0.25)
+
+ * work dir now automatically set to temp dir when not given
+ * introduced translate-jobid-in-param-values param to suppress unexpected file name (and other) conversions - now you have to explicitly ask for this behaviour
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Fri, 27 Aug 2010 17:33:30 +0200
+
+profphd (1.0.24)
+
+ * Man page syntax corrected
+ * Better debugging output
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Fri, 27 Aug 2010 17:33:30 +0200
+
+profphd (1.0.23)
+
+ * Now the default is to no change nice level
+ * Documented para3 paraBoth paraSec paraAcc numresMin nresPerLineAli riSubSec riSubAcc riSubSym
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Mon, 23 Aug 2010 20:48:29 +0200
+
+profphd (1.0.22)
+
+ * Documented a phd.pl call
+ * Fixed overzealous ID substitution in src/prof/embl/scr/lib-phd.pl
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Mon, 05 Jul 2010 12:25:14 +0200
+
+profphd (1.0.21)
+
+ * Fixed verbosity bug that lead to incorrect call to hssp_filter.pl
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Thu, 24 Jun 2010 14:54:11 +0200
+
+profphd (1.0.20)
+
+ * Changed default to silent mode from verbose
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Thu, 24 Jun 2010 11:56:26 +0200
+
+profphd (1.0.19)
+
+ * Added param dirWork to prof/scr/lib/lib-prof.pl exeCopf call
+ * Markus' failing sequence now works ('ARCH' in file name problem)
+ * Weird prof/scr/lib/lib-prof.pl $fileOut{1,$kwd} constructs eliminated
+ * Resolved bug 9 'prof creates tmp files into current directory (where it is run from)'
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Sat, 15 May 2010 13:38:56 +0200
+
+profphd (1.0.18)
+
+ * resolved bug #10 html formatting of ouput
+
+ -- Guy Yachdav <gyachdav at rostlab.org> Sun, 02 May 2010 13:28:27 +0200
+
+profphd (1.0.17)
+
+ * Much more efficient install Makefile target
+ * Produces gold standard for tsnap_query.fasta
+ * Able to use dirWork now: read-only input file dir is now OK
+ * Command line options now correctly documented: no leading -
+ * sed --in-place -> -i, --in-place is not understood by Mac sed
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Sat, 15 May 2010 13:38:41 +0200
+
+profphd (1.0.16)
+
+ * corrected faulty file name extension matching: escapes '.' now
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Tue, 09 Feb 2010 18:18:43 +0100
+
+profphd (1.0.15)
+
+ * removed pub blast - it was not in use
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Sat, 16 Jan 2010 11:03:59 +0100
+
+profphd (1.0.14)
+
+ * moved ./src/prof/scr/safFilterRed.pl to librg-utils-perl
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Fri, 15 Jan 2010 16:00:43 +0100
+
+profphd (1.0.13)
+
+ * Modifications now allow usage of RG::Utils::* modules
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Thu, 14 Jan 2010 21:10:39 +0100
+
+profphd (1.0.12)
+
+ * added debugging for system()-like calls to scr/pack/hssp_filter.pm
+ * added more examples: DMD_HUMAN.hssp is huge; PSA2_HUMAN.safFil has xxxx_a and xxxx_A sequences;
+ * increased MAXCORE to 16777216 in filter_hssp.f in order to allow a big alignment to fit (DMD_HUMAN.hssp example)
+ * Made sequence names case sensitive for READ_MSF routine - solves bug with 3h4p_A and 3h4p_a chains mistaken for the same thing
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Tue, 12 Jan 2010 11:52:56 +0100
+
+profphd (1.0.11)
+
+ * Fixed hssp_filter 'gyachdav' path bug
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Fri, 08 Jan 2010 12:49:19 +0100
+
+profphd (1.0.10)
+
+ * Removed faulty executable checks that did not take PATH into account
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Thu, 07 Jan 2010 18:24:46 +0100
+
+profphd (1.0.9)
+
+ * Removed bin dependency of make all target because the binary utilities are distributed in a separate package
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Thu, 07 Jan 2010 15:06:40 +0100
+
+profphd (1.0.8)
+
+ * Removed $ARCH extension from src/prof/scr/pack/copf.pm exeConvertSeq and exeConvertSeqBig
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Thu, 07 Jan 2010 10:18:44 +0100
+
+profphd (1.0.7)
+
+ * Fixed saf issue due to copf path problem
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Wed, 06 Jan 2010 17:01:59 +0100
+
+profphd (1.0.6)
+
+ * Changed prof to the gold-standard: the prof from SNAP (now snapfun)
+ * Introduces __PREFIX__ where necessary
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Tue, 05 Jan 2010 21:51:16 +0100
+
+profphd (1.0.5)
+
+ * Moved prof and phd fortran sources to profnet package
+ * Added facilities for making a Debian source package out of src-lib
+ * Changed prof to the gold-standard: the prof from SNAP (now snapfun)
+ * Introduces __PREFIX__ where necessary
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Tue, 05 Jan 2010 21:51:16 +0100
+
+profphd (1.0.4)
+
+ * Added -fbounds-check to Fortran compilation options
+ * Removed .LINUX from binary names
+ * Fixed string bounds problem at line 327 of file lib-phd.f
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Tue, 15 Dec 2009 23:57:05 +0100
+
+profphd (1.0.3)
+
+ * Adjusted buffer size for reading in network data. Allows for analysis of large (>2000 residues) sequences
+
+ -- Guy Yachdav <gyachdav at rostlab.org> Tue, 24 Nov 2009 12:22:17 +0200
+
+profphd (1.0.2)
+
+ * Compilation failure when profphd is installed on system issue resolved.
+ * Man page example changed to work in default installation scenario.
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Fri, 20 Nov 2009 08:15:04 +0100
+
Added: trunk/packages/rostlab/profphd/trunk/debian/compat
===================================================================
--- trunk/packages/rostlab/profphd/trunk/debian/compat (rev 0)
+++ trunk/packages/rostlab/profphd/trunk/debian/compat 2011-09-27 15:29:37 UTC (rev 7956)
@@ -0,0 +1 @@
+7
Added: trunk/packages/rostlab/profphd/trunk/debian/control
===================================================================
--- trunk/packages/rostlab/profphd/trunk/debian/control (rev 0)
+++ trunk/packages/rostlab/profphd/trunk/debian/control 2011-09-27 15:29:37 UTC (rev 7956)
@@ -0,0 +1,48 @@
+Source: profphd
+Section: science
+Priority: extra
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Laszlo Kajan <lkajan at rostlab.org>
+Build-Depends: cdbs, debhelper (>= 7.0.50~), perl
+Standards-Version: 3.9.2
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/rostlab/profphd/trunk/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/rostlab/profphd/trunk/
+DM-Upload-Allowed: yes
+Homepage: http://www.rostlab.org/
+
+Package: profphd
+Architecture: all
+Depends: ${perl:Depends}, ${misc:Depends}, librg-utils-perl (>= 1.0.16), profnet-prof, profphd-utils, profphd-net
+Replaces: profphd-data, profphd-perl
+Conflicts: profphd-data, profphd-perl
+Description: secondary structure and solvent accessibility predictor
+ Solvent accessibility is predicted by a neural network method rating at a
+ correlation coefficient (correlation between experimentally observed and
+ predicted relative solvent accessibility) of 0.54 cross-validated on a set of
+ 238 globular proteins (Rost & Sander, Proteins, 1994, 20, 216-226;
+ evaluation of accuracy). The output of the neural network codes for 10 states
+ of relative accessibility. Expressed in units of the difference between
+ prediction by homology modelling (best method) and prediction at random
+ (worst method), PROFacc is some 26 percentage points superior to a comparable
+ neural network using three output states (buried, intermediate, exposed) and
+ using no information from multiple alignments.
+ .
+ Transmembrane helices
+ in integral membrane proteins are predicted by a system of neural networks.
+ The shortcoming of the network system is that often too long helices are
+ predicted. These are cut by an empirical filter. The final prediction
+ (Rost et al., Protein Science, 1995, 4, 521-533; evaluation of accuracy)
+ has an expected per-residue accuracy of about 95%. The number of false
+ positives, i.e., transmembrane helices predicted in globular proteins, is
+ about 2%.
+ .
+ The neural network prediction of transmembrane helices
+ (PHDhtm) is refined by a dynamic programming-like algorithm. This method
+ resulted in correct predictions of all transmembrane helices for 89% of the
+ 131 proteins used in a cross-validation test; more than 98% of the
+ transmembrane helices were correctly predicted. The output of this method
+ is used to predict topology, i.e., the orientation of the N-term with respect
+ to the membrane. The expected accuracy of the topology prediction is > 86%.
+ Prediction accuracy is higher than average for eukaryotic proteins and lower
+ than average for prokaryotes. PHDtopology is more accurate than all other
+ methods tested on identical data sets.
Added: trunk/packages/rostlab/profphd/trunk/debian/copyright
===================================================================
--- trunk/packages/rostlab/profphd/trunk/debian/copyright (rev 0)
+++ trunk/packages/rostlab/profphd/trunk/debian/copyright 2011-09-27 15:29:37 UTC (rev 7956)
@@ -0,0 +1,50 @@
+This package was debianized by Laszlo Kajan <lkajan at rostlab.org> on
+
+ Tue, 17 Nov 2009 10:50:19 +0100.
+
+It was downloaded from:
+
+ ftp://rostlab.org/profphd-utils/
+
+Upstream Authors:
+
+ B. Rost <rost at rostlab.org>
+ C. Sander
+ P. Fariselli
+ R. Casadio
+ J. Liu
+ G. Yachdav <gyachdav at rostlab.org>
+ L. Kajan <lkajan at rostlab.org>
+
+Copyright:
+
+ Copyright 1998 by Burkhard Rost <rost at rostlab.org> EMBL, CUBIC (Columbia University, NY, USA) and LION Biosciences (Heidelberg, DE)
+
+ Copyright 2009-2011 by Laszlo Kajan <lkajan at rostlab.org> Technical University Munich (Munich, DE)
+
+ Copyright 2009-2011 by Guy Yachdav <gyachdav at rostlab.org> CUBIC (Columbia University, NY, USA) and Technical University Munich (Munich, DE)
+
+License:
+
+ This package 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 2 of the License, or
+ (at your option) any later version.
+
+ This package 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 package; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+
+On Debian systems, the complete text of the GNU General
+Public License version 2 can be found in `/usr/share/common-licenses/GPL-2'.
+
+The Debian packaging is:
+
+ (C) 2009, Laszlo Kajan <lkajan at rostlab.org>
+
+and is licensed under the GPL, see above.
Added: trunk/packages/rostlab/profphd/trunk/debian/profphd.install
===================================================================
--- trunk/packages/rostlab/profphd/trunk/debian/profphd.install (rev 0)
+++ trunk/packages/rostlab/profphd/trunk/debian/profphd.install 2011-09-27 15:29:37 UTC (rev 7956)
@@ -0,0 +1 @@
+usr/*
Added: trunk/packages/rostlab/profphd/trunk/debian/rules
===================================================================
--- trunk/packages/rostlab/profphd/trunk/debian/rules (rev 0)
+++ trunk/packages/rostlab/profphd/trunk/debian/rules 2011-09-27 15:29:37 UTC (rev 7956)
@@ -0,0 +1,8 @@
+#!/usr/bin/make -f
+
+include /usr/share/cdbs/1/rules/debhelper.mk
+include /usr/share/cdbs/1/class/makefile.mk
+
+# Add here any variable or target overrides you need.
+DEB_MAKE_BUILD_TARGET = prefix=/usr all
+DEB_MAKE_INSTALL_TARGET = prefix=/usr DESTDIR=$(CURDIR)/debian/tmp/ install
Property changes on: trunk/packages/rostlab/profphd/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/rostlab/profphd/trunk/debian/source/format
===================================================================
--- trunk/packages/rostlab/profphd/trunk/debian/source/format (rev 0)
+++ trunk/packages/rostlab/profphd/trunk/debian/source/format 2011-09-27 15:29:37 UTC (rev 7956)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/rostlab/profphd/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/rostlab/profphd/trunk/debian/upstream-metadata.yaml (rev 0)
+++ trunk/packages/rostlab/profphd/trunk/debian/upstream-metadata.yaml 2011-09-27 15:29:37 UTC (rev 7956)
@@ -0,0 +1,29 @@
+Name: profphd
+Reference:
+ - Author: Rost, B. and Sander, C.
+ Title: 'Combining evolutionary information and neural networks to predict protein secondary structure.'
+ Journal: Proteins
+ Volume: 19
+ Number: 1
+ Pages: 55-72
+ Year: 1994
+ URL: http://rostlab.org/
+ PMID: 8066087
+ - Author: Rost, B. and Sander, C.
+ Title: 'Conservation and prediction of solvent accessibility in protein families.'
+ Journal: Proteins
+ Volume: 20
+ Number: 3
+ Pages: 216-26
+ Year: 1994
+ URL: http://rostlab.org/
+ PMID: 7892171
+ - Author: Rost, B., Casadio, R., Fariselli, P., and Sander, C.
+ Title: 'Transmembrane helices predicted at 95% accuracy.'
+ Journal: Protein Sci
+ Volume: 4
+ Number: 3
+ Pages: 521-33
+ Year: 1995
+ URL: http://rostlab.org/
+ PMID: 7795533
Added: trunk/packages/rostlab/profphd/trunk/debian/watch
===================================================================
--- trunk/packages/rostlab/profphd/trunk/debian/watch (rev 0)
+++ trunk/packages/rostlab/profphd/trunk/debian/watch 2011-09-27 15:29:37 UTC (rev 7956)
@@ -0,0 +1,23 @@
+# Example watch control file for uscan
+# Rename this file to "watch" and then you can run the "uscan" command
+# to check for upstream updates and more.
+# See uscan(1) for format
+
+# Compulsory line, this is a version 3 file
+version=3
+
+# Uncomment to examine a Webpage
+# <Webpage URL> <string match>
+#http://www.example.com/downloads.php libzerg-perl-(.*)\.tar\.gz
+
+# Uncomment to examine a Webserver directory
+#http://www.example.com/pub/libzerg-perl-(.*)\.tar\.gz
+
+# Uncommment to examine a FTP server
+ftp://rostlab.org/profphd/profphd-(.*)\.tar\.gz debian uupdate
+
+# Uncomment to find new files on sourceforge, for devscripts >= 2.9
+# http://sf.net/libzerg-perl/libzerg-perl-(.*)\.tar\.gz
+
+# Uncomment to find new files on GooglePages
+#http://code.google.com/p/libzerg/downloads/list libzerg-perl[_-](.*)\.tar\.gz
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