[med-svn] [profit] 01/11: This package is nothing for Debian Med itself, it is just another one of those that come with source code (and consequently should be rebuildable with our distribution) but are not redistributable.
Andreas Tille
tille at debian.org
Mon Dec 18 19:57:27 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository profit.
commit 645ae167a2a80c2578a3c80f0e6b8437ac785489
Author: Steffen Moeller <moeller at debian.org>
Date: Wed Jun 5 16:19:05 2013 +0000
This package is nothing for Debian Med itself, it is just another
one of those that come with source code (and consequently should
be rebuildable with our distribution) but are not redistributable.
ProFit is (sadly) a common tool in structural biology to align
two proteins. If I recall correctly (and things have not changed)
then it all starts with the centers of gravity plus a three dimensional
turning along what a sequence alignment gives us.
---
debian/README.Debian | 9 ++++
debian/README.source | 9 ++++
debian/changelog | 5 +++
debian/compat | 1 +
debian/control | 21 +++++++++
debian/copyright | 73 +++++++++++++++++++++++++++++++
debian/docs | 4 ++
debian/patches/AllowReadline.patch | 15 +++++++
debian/patches/AllowRedundantCleans.patch | 13 ++++++
debian/patches/series | 2 +
debian/profit-data.dirs | 1 +
debian/profit-data.install | 2 +
debian/profit.dirs | 1 +
debian/profit.install | 2 +
debian/profit.sh | 5 +++
debian/rules | 20 +++++++++
debian/source/format | 1 +
17 files changed, 184 insertions(+)
diff --git a/debian/README.Debian b/debian/README.Debian
new file mode 100644
index 0000000..72fe1e1
--- /dev/null
+++ b/debian/README.Debian
@@ -0,0 +1,9 @@
+profit for Debian
+-----------------
+
+The license of ProFit does not allow a redistribution.
+
+The documentation is not built, since it demanded too much of LaTeX to be installed,
+also for a conversion to HTML. It ships with the original source code.
+
+ -- Steffen Moeller <moeller at debian.org> Wed, 05 Jun 2013 17:38:14 +0200
diff --git a/debian/README.source b/debian/README.source
new file mode 100644
index 0000000..54070d4
--- /dev/null
+++ b/debian/README.source
@@ -0,0 +1,9 @@
+profit for Debian
+-----------------
+
+<this file describes information about the source package, see Debian policy
+manual section 4.14. You WILL either need to modify or delete this file>
+
+
+
+
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..56c0f7f
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+profit (3.1-1) UNRELEASED; urgency=low
+
+ * The license does not allow a redistribution.
+
+ -- Steffen Moeller <moeller at debian.org> Wed, 05 Jun 2013 17:38:14 +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..79c9bc7
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,21 @@
+Source: profit
+Section: non-free/science
+Priority: optional
+Maintainer: Steffen Moeller <steffen_moeller at gmx.de>
+Build-Depends: debhelper (>= 8.0.0), libreadline-dev
+Standards-Version: 3.9.4
+Homepage: http://www.bioinf.org.uk/software/profit/
+#Vcs-Git: git://git.debian.org/collab-maint/profit.git
+#Vcs-Browser: http://git.debian.org/?p=collab-maint/profit.git;a=summary
+
+Package: profit
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}, profit-data
+Description: Protein structure alignment
+ Nothing to be redistributed.
+
+Package: profit-data
+Architecture: all
+Recommends: profit
+Description: Help and data files for Profit
+ Nothing to be redistributed.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..9aab3a1
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,73 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: profit
+Source: <url://example.com>
+
+Files: *
+Copyright: <years> <put author's name and email here>
+ <years> <likewise for another author>
+License: <special license>
+ ProFit
+ .
+ Protein Least Squares Fitting
+ .
+ .
+ .
+ .
+ ProFit is copyright Dr. Andrew C.R. Martin, SciTech Software and
+ UCL 1992-2009
+ Dr. Craig Porter, UCL 2008-2009
+ Modifications and enhancements were also made while working at
+ The University of Reading under consultancy to Inpharmatica, Ltd.
+ Development of V2.6-V3.1 was funded by the BBSRC
+ .
+ This program is not in the public domain.
+ .
+ It may not be copied or made available to third parties, but may be
+ freely used by anyone who has obtained it directly from the author's
+ Web Site. Please register your name and email address on the web site
+ when you download the software.
+ .
+ The code may not be made available on other FTP sites without express
+ permission from the author.
+ .
+ The code may be modified as required, but any modifications must be
+ documented so that the person responsible can be identified. If
+ someone else breaks this code, the author doesn't want to be blamed
+ for code that does not work! You may not distribute any
+ modifications, but are encouraged to send them to the author so
+ that they may be incorporated into future versions of the code.
+ .
+ The code may not be sold commercially, but the program may be used for
+ commercial purposes.
+ .
+ IN NO EVENT SHALL THE AUTHOR OR ANY INSTITUTION IN WHICH HE IS WORKING
+ (INCLUDING, BUT NOT LIMITED TO, UNIVERSITY COLLEGE LONDON) BE LIABLE
+ TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL
+ DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF THIS SOFTWARE
+ AND ITS DOCUMENTATION, EVEN IF THE AUTHOR HAS BEEN ADVISED OF THE
+ POSSIBILITY OF SUCH DAMAGE.
+ .
+ THE AUTHOR SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT
+ LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+ A PARTICULAR PURPOSE. THE SOFTWARE PROVIDED HEREUNDER IS ON AN "AS IS"
+ BASIS, AND THE AUTHOR HAS NO OBLIGATIONS TO PROVIDE MAINTENANCE, SUPPORT,
+ UPDATES, ENHANCEMENTS, OR MODIFICATIONS.
+
+Files: debian/*
+Copyright: 2013 Steffen Moeller <steffen_moeller at gmx.de>
+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/docs b/debian/docs
new file mode 100644
index 0000000..70d0f4c
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1,4 @@
+DOS.txt
+HISTORY
+INSTALL
+00Read.Me
diff --git a/debian/patches/AllowReadline.patch b/debian/patches/AllowReadline.patch
new file mode 100644
index 0000000..02b9e80
--- /dev/null
+++ b/debian/patches/AllowReadline.patch
@@ -0,0 +1,15 @@
+Index: profit-3.1/src/Makefile
+===================================================================
+--- profit-3.1.orig/src/Makefile
++++ profit-3.1/src/Makefile
+@@ -6,8 +6,8 @@
+ # To allow use of the GNU Readline library, uncomment the following two
+ # lines - You may need to install the GNU readline development libraries
+ # first!
+-#READLINE = -DREADLINE_SUPPORT
+-#READLINELIB = -lreadline -lcurses
++READLINE = -DREADLINE_SUPPORT
++READLINELIB = -lreadline -lcurses
+
+ # Uncomment if you want to use the rotate and refit code for avoiding
+ # local minimum problem. If compiled with gcc -O3 this problem seems to
diff --git a/debian/patches/AllowRedundantCleans.patch b/debian/patches/AllowRedundantCleans.patch
new file mode 100644
index 0000000..d2ccd9f
--- /dev/null
+++ b/debian/patches/AllowRedundantCleans.patch
@@ -0,0 +1,13 @@
+Index: profit-3.1/src/Makefile
+===================================================================
+--- profit-3.1.orig/src/Makefile
++++ profit-3.1/src/Makefile
+@@ -54,7 +54,7 @@
+ $(CC) $(COPT) $(READLINE) $(ROTATEREFIT) -o $@ -c $<
+
+ clean :
+- /bin/rm $(OFILES) $(LFILES)
++ /bin/rm -f $(OFILES) $(LFILES)
+
+ protos : $(PFILES)
+
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..57acc99
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,2 @@
+AllowReadline.patch
+AllowRedundantCleans.patch
diff --git a/debian/profit-data.dirs b/debian/profit-data.dirs
new file mode 100644
index 0000000..358de10
--- /dev/null
+++ b/debian/profit-data.dirs
@@ -0,0 +1 @@
+usr/share/profit
diff --git a/debian/profit-data.install b/debian/profit-data.install
new file mode 100644
index 0000000..b7b3ef6
--- /dev/null
+++ b/debian/profit-data.install
@@ -0,0 +1,2 @@
+mdm78.mat usr/share/profit/
+ProFit.help usr/share/profit/
diff --git a/debian/profit.dirs b/debian/profit.dirs
new file mode 100644
index 0000000..66bd4fb
--- /dev/null
+++ b/debian/profit.dirs
@@ -0,0 +1 @@
+usr/lib/profit
diff --git a/debian/profit.install b/debian/profit.install
new file mode 100644
index 0000000..c4e0e66
--- /dev/null
+++ b/debian/profit.install
@@ -0,0 +1,2 @@
+src/profit usr/lib/profit/
+debian/profit.sh usr/bin/profit
diff --git a/debian/profit.sh b/debian/profit.sh
new file mode 100755
index 0000000..0148339
--- /dev/null
+++ b/debian/profit.sh
@@ -0,0 +1,5 @@
+#!/bin/sh
+
+export HELPDIR=/usr/share/profit/
+export DATADIR=/usr/share/profit/
+/usr/lib/profit/profit $*
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..99bc6ec
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,20 @@
+#!/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
+
+%:
+ dh $@
+
+override_dh_auto_build:
+ $(MAKE) -C src
+
+override_dh_auto_clean:
+ $(MAKE) -C src clean
+
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)
--
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