[med-svn] [psipred] 01/15: 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.
Andreas Tille
tille at debian.org
Mon Dec 18 20:32:21 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository psipred.
commit d6646ec6b581619ca50fb783a9de2ba3fce922d4
Author: Steffen Moeller <moeller at debian.org>
Date: Fri Aug 3 14:32:48 2012 +0000
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
---
debian/README.Debian | 8 +++
debian/README.source | 13 +++++
debian/changelog | 6 ++
debian/compat | 1 +
debian/control | 34 +++++++++++
debian/copyright | 115 +++++++++++++++++++++++++++++++++++++
debian/patches/Makefile.patch | 42 ++++++++++++++
debian/patches/runpsipred.patch | 122 ++++++++++++++++++++++++++++++++++++++++
debian/patches/series | 2 +
debian/psipred-data.install | 1 +
debian/psipred.docs | 3 +
debian/psipred.examples | 4 ++
debian/psipred.install | 4 ++
debian/psipred.links | 1 +
debian/rules | 18 ++++++
debian/source/format | 1 +
debian/watch | 2 +
17 files changed, 377 insertions(+)
diff --git a/debian/README.Debian b/debian/README.Debian
new file mode 100644
index 0000000..69eb827
--- /dev/null
+++ b/debian/README.Debian
@@ -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 <moeller at debian.org> Fri, 03 Aug 2012 14:33:00 +0200
diff --git a/debian/README.source b/debian/README.source
new file mode 100644
index 0000000..6baf28c
--- /dev/null
+++ b/debian/README.source
@@ -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.
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..8c563af
--- /dev/null
+++ b/debian/changelog
@@ -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 <moeller at debian.org> Fri, 03 Aug 2012 14:33:00 +0200
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..45a4fb7
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+8
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..1166227
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,34 @@
+Source: psipred
+Section: non-free/science
+Priority: extra
+Maintainer: Steffen Moeller <moeller at debian.org>
+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.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..d168a30
--- /dev/null
+++ b/debian/copyright
@@ -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: dtj at cs.ucl.ac.uk
+ .
+ * 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 <moeller at debian.org>
+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".
diff --git a/debian/patches/Makefile.patch b/debian/patches/Makefile.patch
new file mode 100644
index 0000000..0bce847
--- /dev/null
+++ b/debian/patches/Makefile.patch
@@ -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
diff --git a/debian/patches/runpsipred.patch b/debian/patches/runpsipred.patch
new file mode 100644
index 0000000..9bed490
--- /dev/null
+++ b/debian/patches/runpsipred.patch
@@ -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."
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..02e8c91
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,2 @@
+runpsipred.patch
+Makefile.patch
diff --git a/debian/psipred-data.install b/debian/psipred-data.install
new file mode 100644
index 0000000..250fe5e
--- /dev/null
+++ b/debian/psipred-data.install
@@ -0,0 +1 @@
+data usr/share/psipred
diff --git a/debian/psipred.docs b/debian/psipred.docs
new file mode 100644
index 0000000..18d94ee
--- /dev/null
+++ b/debian/psipred.docs
@@ -0,0 +1,3 @@
+README
+BLAST+/README
+VERSION
diff --git a/debian/psipred.examples b/debian/psipred.examples
new file mode 100644
index 0000000..aebfb58
--- /dev/null
+++ b/debian/psipred.examples
@@ -0,0 +1,4 @@
+example.fasta
+example.horiz
+example.ss
+example.ss2
diff --git a/debian/psipred.install b/debian/psipred.install
new file mode 100644
index 0000000..d4a0007
--- /dev/null
+++ b/debian/psipred.install
@@ -0,0 +1,4 @@
+bin/* usr/lib/psipred/bin
+runpsipred usr/bin
+runpsipred_single usr/bin
+BLAST+/runpsipredplus usr/bin
diff --git a/debian/psipred.links b/debian/psipred.links
new file mode 100644
index 0000000..aa50d9a
--- /dev/null
+++ b/debian/psipred.links
@@ -0,0 +1 @@
+usr/lib/psipred/bin usr/share/psipred/bin
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..75a9daf
--- /dev/null
+++ b/debian/rules
@@ -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
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..fb798ef
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,2 @@
+version=3
+http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/psipred(.*)\.tar\.gz
--
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