Author: moeller Date: 2012-08-03 14:32:48 +0000 (Fri, 03 Aug 2012) New Revision: 11983
Added: trunk/packages/psipred/ trunk/packages/psipred/trunk/ trunk/packages/psipred/trunk/debian/ trunk/packages/psipred/trunk/debian/README.Debian trunk/packages/psipred/trunk/debian/README.source trunk/packages/psipred/trunk/debian/changelog trunk/packages/psipred/trunk/debian/compat trunk/packages/psipred/trunk/debian/control trunk/packages/psipred/trunk/debian/copyright trunk/packages/psipred/trunk/debian/patches/ trunk/packages/psipred/trunk/debian/patches/Makefile.patch trunk/packages/psipred/trunk/debian/patches/runpsipred.patch trunk/packages/psipred/trunk/debian/patches/series trunk/packages/psipred/trunk/debian/psipred-data.install trunk/packages/psipred/trunk/debian/psipred.docs trunk/packages/psipred/trunk/debian/psipred.examples trunk/packages/psipred/trunk/debian/psipred.install trunk/packages/psipred/trunk/debian/psipred.links trunk/packages/psipred/trunk/debian/rules trunk/packages/psipred/trunk/debian/source/ trunk/packages/psipred/trunk/debian/source/format trunk/packages/psipred/trunk/debian/watch Log: Adding build instructions for psipred - another of those tools besides VMD or Rosetta that cannot be redistributed in our distribution but ships with source code. No idea why it is so picky about the hardening. I thought to have addressed it ... well, ... days are limited. W: psipred-data: new-package-should-close-itp-bug W: psipred-dbg: new-package-should-close-itp-bug W: psipred: hardening-no-fortify-functions usr/lib/psipred/bin/chkparse W: psipred: hardening-no-fortify-functions usr/lib/psipred/bin/pfilt W: psipred: hardening-no-fortify-functions usr/lib/psipred/bin/psipass2 W: psipred: hardening-no-fortify-functions usr/lib/psipred/bin/psipred W: psipred: hardening-no-fortify-functions usr/lib/psipred/bin/seq2mtx W: psipred: new-package-should-close-itp-bug W: psipred: binary-without-manpage usr/bin/runpsipred W: psipred: binary-without-manpage usr/bin/runpsipred_single W: psipred: binary-without-manpage usr/bin/runpsipredplus W: psipred: csh-considered-harmful usr/bin/runpsipred W: psipred: csh-considered-harmful usr/bin/runpsipred_single W: psipred: csh-considered-harmful usr/bin/runpsipredplus Property changes on: trunk/packages/psipred/trunk/debian ___________________________________________________________________ Added: mergeWithUpstream + 1 Added: trunk/packages/psipred/trunk/debian/README.Debian =================================================================== --- trunk/packages/psipred/trunk/debian/README.Debian (rev 0) +++ trunk/packages/psipred/trunk/debian/README.Debian 2012-08-03 14:32:48 UTC (rev 11983) @@ -0,0 +1,8 @@ +psipred for Debian +------------------ + +The package build instructions are made available only to help with local orchestration of +PSIPRED installations. It is not meant to insuinate a compatibility of the PSIPRED license +with a redistribution of the binaries. + + -- Steffen Moeller <[email protected]> Fri, 03 Aug 2012 14:33:00 +0200 Added: trunk/packages/psipred/trunk/debian/README.source =================================================================== --- trunk/packages/psipred/trunk/debian/README.source (rev 0) +++ trunk/packages/psipred/trunk/debian/README.source 2012-08-03 14:32:48 UTC (rev 11983) @@ -0,0 +1,13 @@ +psipred for Debian +------------------ + +The following files should be removed from the source distribution +if there ever was a source distribution. + +psipred/bin/chkparse +psipred/bin/seq2mtx +psipred/bin/psipass2 +psipred/bin/psipred +psipred/bin/pfilt + +Patches introduce a toplevel Makefile and adjust paths in the tcsh script. Added: trunk/packages/psipred/trunk/debian/changelog =================================================================== --- trunk/packages/psipred/trunk/debian/changelog (rev 0) +++ trunk/packages/psipred/trunk/debian/changelog 2012-08-03 14:32:48 UTC (rev 11983) @@ -0,0 +1,6 @@ +psipred (3.3-1) UNRELEASED; urgency=low + + * Initial packaging - the package is not meant to be redistributed + because of license restrictions. + + -- Steffen Moeller <[email protected]> Fri, 03 Aug 2012 14:33:00 +0200 Added: trunk/packages/psipred/trunk/debian/compat =================================================================== --- trunk/packages/psipred/trunk/debian/compat (rev 0) +++ trunk/packages/psipred/trunk/debian/compat 2012-08-03 14:32:48 UTC (rev 11983) @@ -0,0 +1 @@ +8 Added: trunk/packages/psipred/trunk/debian/control =================================================================== --- trunk/packages/psipred/trunk/debian/control (rev 0) +++ trunk/packages/psipred/trunk/debian/control 2012-08-03 14:32:48 UTC (rev 11983) @@ -0,0 +1,34 @@ +Source: psipred +Section: non-free/science +Priority: extra +Maintainer: Steffen Moeller <[email protected]> +Build-Depends: debhelper (>= 8.0.0) +Standards-Version: 3.9.3 +Homepage: http://bioinf.cs.ucl.ac.uk/index.php?id=779 +#Vcs-Git: git://git.debian.org/collab-maint/psipred.git +#Vcs-Browser: http://git.debian.org/?p=collab-maint/psipred.git;a=summary + +Package: psipred +Architecture: any +Depends: ${shlibs:Depends}, ${misc:Depends}, blast2, tcsh +Recommends: psipred-data +Description: protein secondary structure prediction + Hm. Someone please provide some text. + +Package: psipred-dbg +Section: non-free/debug +Architecture: any +Depends: ${shlibs:Depends}, ${misc:Depends}, psipred +Description: debug information for psipred + By default, psipred ships without any debug information, + which typically is considered bloat - unless when there + is a problem, this means. Debian has nice ways to separate + the debug information from the remainder of the binary + and add it only on demand. + +Package: psipred-data +Architecture: all +Depends: ${misc:Depends} +Description: data files for psipred + All the architecture-independent files to be placed into + /usr/share/psipred. Added: trunk/packages/psipred/trunk/debian/copyright =================================================================== --- trunk/packages/psipred/trunk/debian/copyright (rev 0) +++ trunk/packages/psipred/trunk/debian/copyright 2012-08-03 14:32:48 UTC (rev 11983) @@ -0,0 +1,115 @@ +Format: http://dep.debian.net/deps/dep5 +Upstream-Name: psipred +Source: http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/ + +Files: * +Copyright: 1995-2012 David T. Jones, UCL, London +License: custom + PLEASE READ THE FOLLOWING LICENSE AGREEMENT. BY USING THE PROGRAM YOU ARE + ACKNOWLEDGING THE FACT THAT YOU AGREE TO THE TERMS OUTLINED IN THIS + AGREEMENT. USERS WISHING TO USE THE SOFTWARE FOR COMMERCIAL ACTIVITIES + NOT COVERED BY THIS AGREEMENT SHOULD SEND E-MAIL TO: [email protected] + . + * NOTE RECENT CHANGES TO PARAGRAPH 8 * + . + . + . + PSIPRED3 - PROTEIN SECONDARY STRUCTURE PREDICTION PROGRAM BY D.T.JONES + ---------------------------------------------------------------------- + . + GENERAL LICENSE & + ----------------- + . + CONFIDENTIALITY AGREEMENT + ------------------------- + . + . + . + In regard to the protein structure prediction program (PSIPRED3) + herewith (the Software) the copyright and other intellectual property + rights to which belong to the Author(s). + . + Any user (the User) of the program undertakes to the Copyright holder that he + or she shall be bound by the following terms and conditions:- + . + 1. The User will receive the Software and any related documentation in + confidence and will not use the same except for the purpose of their own + research. The Software will be used only by such of the User's officers or + employees to whom it must reasonably be communicated to enable them to + undertake their research and who agree to be bound by the same confidence. + The User shall procure and enforce such agreement from his or her staff for + the benefit of the Copyright holder. + . + 2. The publication of research using the Software must include an + appropriate citation to the method: + . + Jones, D.T. (1999) Protein secondary structure prediction based on + position-specific scoring matrices. J. Mol. Biol. 292:195-202. + . + 3. All forms of the Software will be kept in a reasonably secure place to + prevent unauthorised access. + . + 4. Each copy of the Software or, if not practicable then, any package + associated therewith shall be suitably marked (and such marking maintained) + with the following copyright notice: "Copyright 2000 D.T.Jones. All Rights + Reserved.". + . + 5. The Software may be modified, but any changes made shall be communicated + to the Author(s) and made freely available. + . + 6. The Software may not be sold as a standalone package, or incorporated into + a commercial software package without the written permission of the Copyright + holder. The Software may be used freely for individual academic or commercial + research. The Software may also be made freely available for training or + teaching purposes. + . + 7. The results produced by the Software may not be incorporated into any + data banks or databases which are subject to the payment of access or + license fees without the written permission of the Copyright holder. + . + 8. The Software may be made available to users over a local network or + wide area network (including the Internet), but only if access is granted + free of charge to all authorised users. Incorporation of the Software into + a commercial Web site or other fee paying service is not allowed without + the written permission of the Copyright holder. If PSIPRED results are + returned to the user via such a network service, then a suitable + acknowledgement of the PSIPRED method must be returned somewhere in the + output text. + . + 9. The confidentiality obligation in paragraph one shall not apply: + . + (i) to information and data known to the User at the time of + receipt hereunder (as evidenced by its written records); + . + (ii) to information and data which was at the time of receipt in the + public domain or thereafter becomes so through no wrongful act of + the User; + . + (iii) to information and data which the User receives from a third + party not in breach of any obligation of confidentiality owed to + the Author(s). + . + 10. The User understands that the Software is supplied "as is". No warranty + as to its fitness or suitability for any purpose whatsoever is made or + implied. In no event shall the Author(s) or Copyright holder be held + responsible for any direct or indirect damages arising through the use + of the Software. + +Files: debian/* +Copyright: 2012 Steffen Moeller <[email protected]> +License: GPL-2+ + 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 program. If not, see <http://www.gnu.org/licenses/> + . + On Debian systems, the complete text of the GNU General + Public License version 2 can be found in "/usr/share/common-licenses/GPL-2". Added: trunk/packages/psipred/trunk/debian/patches/Makefile.patch =================================================================== --- trunk/packages/psipred/trunk/debian/patches/Makefile.patch (rev 0) +++ trunk/packages/psipred/trunk/debian/patches/Makefile.patch 2012-08-03 14:32:48 UTC (rev 11983) @@ -0,0 +1,42 @@ +Index: psipred-3.3/Makefile +=================================================================== +--- /dev/null 1970-01-01 00:00:00.000000000 +0000 ++++ psipred-3.3/Makefile 2012-08-03 16:23:59.996061035 +0200 +@@ -0,0 +1,4 @@ ++ ++all %: ++ $(MAKE) -C src $@ ++ +Index: psipred-3.3/src/Makefile +=================================================================== +--- psipred-3.3.orig/src/Makefile 2012-08-03 16:04:09.736181254 +0200 ++++ psipred-3.3/src/Makefile 2012-08-03 16:27:02.889586647 +0200 +@@ -6,9 +6,9 @@ + #### CFLAGS Flags to pass to C compiler. + + INCDIR = . +-CC = cc ++CC = gcc + +-CFLAGS = -O ++CFLAGS = $(shell dpkg-buildflags --get CFLAGS) -Wl,-z,relro + LIBS = -lm + + all: psipred psipass2 chkparse seq2mtx pfilt +@@ -16,7 +16,7 @@ + install: + /bin/cp psipred psipass2 chkparse seq2mtx pfilt ../bin + +-clean: ++distclean clean: + /bin/rm -f psipred psipass2 chkparse seq2mtx pfilt + + psipred: sspred_avpred.c ssdefs.h sspred_net.h +@@ -33,3 +33,7 @@ + + pfilt: pfilt.c + $(CC) $(CFLAGS) pfilt.c $(LIBS) -o pfilt ++ ++test: ++ ++.PHONY: test distclean clean install all Added: trunk/packages/psipred/trunk/debian/patches/runpsipred.patch =================================================================== --- trunk/packages/psipred/trunk/debian/patches/runpsipred.patch (rev 0) +++ trunk/packages/psipred/trunk/debian/patches/runpsipred.patch 2012-08-03 14:32:48 UTC (rev 11983) @@ -0,0 +1,122 @@ +Index: psipred-3.3/BLAST+/runpsipredplus +=================================================================== +--- psipred-3.3.orig/BLAST+/runpsipredplus 2012-08-03 16:18:43.868344439 +0200 ++++ psipred-3.3/BLAST+/runpsipredplus 2012-08-03 16:21:12.938324484 +0200 +@@ -1,4 +1,4 @@ +-#!/bin/tcsh ++#!/usr/bin/tcsh + + # This is a simple script which will carry out all of the basic steps + # required to make a PSIPRED V3 prediction using BLAST+. Note that it +@@ -14,13 +14,13 @@ + set dbname = uniref90filt + + # Where the NCBI BLAST+ programs have been installed +-set ncbidir = /usr/local/bin ++set ncbidir = /usr/bin + + # Where the PSIPRED V3 programs have been installed +-set execdir = ../bin ++set execdir = /usr/lib/psipred/bin + + # Where the PSIPRED V3 data files have been installed +-set datadir = ../data ++set datadir = /usr/share/psipred/data + + set basename = $1:r + set rootname = $basename:t +@@ -29,7 +29,7 @@ + set hostid = `hostid` + set tmproot = psitmp$$$hostid + +-\cp -f $1 $tmproot.fasta ++cp -f $1 $tmproot.fasta + + echo "Running PSI-BLAST with sequence" $1 "..." + +@@ -71,7 +71,7 @@ + # Remove temporary files + + echo Cleaning up ... +-\rm -f $tmproot.* error.log ++rm -f $tmproot.* error.log + + echo "Final output files:" $rootname.ss2 $rootname.horiz + echo "Finished." +Index: psipred-3.3/runpsipred +=================================================================== +--- psipred-3.3.orig/runpsipred 2012-08-03 16:18:43.868344439 +0200 ++++ psipred-3.3/runpsipred 2012-08-03 16:20:52.302604094 +0200 +@@ -1,4 +1,4 @@ +-#!/bin/tcsh ++#!/usr/bin/tcsh + + # This is a simple script which will carry out all of the basic steps + # required to make a PSIPRED V2 prediction. Note that it assumes that the +@@ -15,13 +15,13 @@ + set dbname = swiss + + # Where the NCBI programs have been installed +-set ncbidir = /usr/local/bin ++set ncbidir = /usr/bin + + # Where the PSIPRED V2 programs have been installed +-set execdir = ./bin ++set execdir = /usr/lib/psipred/bin + + # Where the PSIPRED V2 data files have been installed +-set datadir = ./data ++set datadir = /usr/share/psipred/data + + set basename = $1:r + set rootname = $basename:t +@@ -30,7 +30,7 @@ + set hostid = `hostid` + set tmproot = psitmp$$$hostid + +-\cp -f $1 $tmproot.fasta ++cp -f $1 $tmproot.fasta + + echo "Running PSI-BLAST with sequence" $1 "..." + +@@ -75,7 +75,7 @@ + # Remove temporary files + + echo Cleaning up ... +-\rm -f $tmproot.* error.log ++rm -f $tmproot.* error.log + + echo "Final output files:" $rootname.ss2 $rootname.horiz + echo "Finished." +Index: psipred-3.3/runpsipred_single +=================================================================== +--- psipred-3.3.orig/runpsipred_single 2012-08-03 16:18:43.868344439 +0200 ++++ psipred-3.3/runpsipred_single 2012-08-03 16:21:21.058214463 +0200 +@@ -1,4 +1,4 @@ +-#!/bin/tcsh ++#!/usr/bin/tcsh + + # This is a simple script which will carry out all of the basic steps + # required to make a PSIPRED prediction. Note that it assumes that the +@@ -10,10 +10,10 @@ + # NOTE: Script modified to be more cluster friendly (DTJ April 2008) + + # Where the PSIPRED V3 programs have been installed +-set execdir = ./bin ++set execdir = /usr/lib/psipred/bin + + # Where the PSIPRED V3 data files have been installed +-set datadir = ./data ++set datadir = /usr/share/psipred/data + + set basename = $1:r + set rootname = $basename:t +@@ -55,7 +55,7 @@ + # Remove temporary files + + echo Cleaning up ... +-\rm -f $tmproot.* error.log ++rm -f $tmproot.* error.log + + echo "Final output files:" $rootname.ss2 $rootname.horiz + echo "Finished." Added: trunk/packages/psipred/trunk/debian/patches/series =================================================================== --- trunk/packages/psipred/trunk/debian/patches/series (rev 0) +++ trunk/packages/psipred/trunk/debian/patches/series 2012-08-03 14:32:48 UTC (rev 11983) @@ -0,0 +1,2 @@ +runpsipred.patch +Makefile.patch Added: trunk/packages/psipred/trunk/debian/psipred-data.install =================================================================== --- trunk/packages/psipred/trunk/debian/psipred-data.install (rev 0) +++ trunk/packages/psipred/trunk/debian/psipred-data.install 2012-08-03 14:32:48 UTC (rev 11983) @@ -0,0 +1 @@ +data usr/share/psipred Added: trunk/packages/psipred/trunk/debian/psipred.docs =================================================================== --- trunk/packages/psipred/trunk/debian/psipred.docs (rev 0) +++ trunk/packages/psipred/trunk/debian/psipred.docs 2012-08-03 14:32:48 UTC (rev 11983) @@ -0,0 +1,3 @@ +README +BLAST+/README +VERSION Added: trunk/packages/psipred/trunk/debian/psipred.examples =================================================================== --- trunk/packages/psipred/trunk/debian/psipred.examples (rev 0) +++ trunk/packages/psipred/trunk/debian/psipred.examples 2012-08-03 14:32:48 UTC (rev 11983) @@ -0,0 +1,4 @@ +example.fasta +example.horiz +example.ss +example.ss2 Added: trunk/packages/psipred/trunk/debian/psipred.install =================================================================== --- trunk/packages/psipred/trunk/debian/psipred.install (rev 0) +++ trunk/packages/psipred/trunk/debian/psipred.install 2012-08-03 14:32:48 UTC (rev 11983) @@ -0,0 +1,4 @@ +bin/* usr/lib/psipred/bin +runpsipred usr/bin +runpsipred_single usr/bin +BLAST+/runpsipredplus usr/bin Added: trunk/packages/psipred/trunk/debian/psipred.links =================================================================== --- trunk/packages/psipred/trunk/debian/psipred.links (rev 0) +++ trunk/packages/psipred/trunk/debian/psipred.links 2012-08-03 14:32:48 UTC (rev 11983) @@ -0,0 +1 @@ +usr/lib/psipred/bin usr/share/psipred/bin Added: trunk/packages/psipred/trunk/debian/rules =================================================================== --- trunk/packages/psipred/trunk/debian/rules (rev 0) +++ trunk/packages/psipred/trunk/debian/rules 2012-08-03 14:32:48 UTC (rev 11983) @@ -0,0 +1,18 @@ +#!/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 + +export DEB_BUILD_HARDENING = 1 + +%: + dh $@ + +override_dh_strip: + dh_strip --dbg-package psipred-dbg Property changes on: trunk/packages/psipred/trunk/debian/rules ___________________________________________________________________ Added: svn:executable + * Added: trunk/packages/psipred/trunk/debian/source/format =================================================================== --- trunk/packages/psipred/trunk/debian/source/format (rev 0) +++ trunk/packages/psipred/trunk/debian/source/format 2012-08-03 14:32:48 UTC (rev 11983) @@ -0,0 +1 @@ +3.0 (quilt) Added: trunk/packages/psipred/trunk/debian/watch =================================================================== --- trunk/packages/psipred/trunk/debian/watch (rev 0) +++ trunk/packages/psipred/trunk/debian/watch 2012-08-03 14:32:48 UTC (rev 11983) @@ -0,0 +1,2 @@ +version=3 +http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/psipred(.*)\.tar\.gz _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
