[med-svn] r9700 - in trunk/packages/sift: . trunk trunk/debian
Laszlo Kajan
lkajan-guest at alioth.debian.org
Fri Feb 17 21:35:37 UTC 2012
Author: lkajan-guest
Date: 2012-02-17 21:35:37 +0000 (Fri, 17 Feb 2012)
New Revision: 9700
Added:
trunk/packages/sift/tags/
trunk/packages/sift/trunk/
trunk/packages/sift/trunk/debian/
trunk/packages/sift/trunk/debian/README.Debian
trunk/packages/sift/trunk/debian/changelog
trunk/packages/sift/trunk/debian/compat
trunk/packages/sift/trunk/debian/control
trunk/packages/sift/trunk/debian/copyright
trunk/packages/sift/trunk/debian/dirs
trunk/packages/sift/trunk/debian/links
trunk/packages/sift/trunk/debian/rules
Modified:
trunk/packages/sift/
Log:
added sift Debianization to repository
Property changes on: trunk/packages/sift
___________________________________________________________________
Added: svn:ignore
+ build-area
tarballs
Property changes on: trunk/packages/sift/trunk/debian
___________________________________________________________________
Added: mergeWithUpstream
+ 1
Added: trunk/packages/sift/trunk/debian/README.Debian
===================================================================
--- trunk/packages/sift/trunk/debian/README.Debian (rev 0)
+++ trunk/packages/sift/trunk/debian/README.Debian 2012-02-17 21:35:37 UTC (rev 9700)
@@ -0,0 +1,6 @@
+sift for Debian
+---------------
+
+This package presents `sift-3.0'. Tested only for FASTA input.
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Mon, 07 Dec 2009 15:22:27 +0100
Added: trunk/packages/sift/trunk/debian/changelog
===================================================================
--- trunk/packages/sift/trunk/debian/changelog (rev 0)
+++ trunk/packages/sift/trunk/debian/changelog 2012-02-17 21:35:37 UTC (rev 9700)
@@ -0,0 +1,5 @@
+sift (3.0-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #????)
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Fri, 17 Feb 2012 22:18:54 +0100
Added: trunk/packages/sift/trunk/debian/compat
===================================================================
--- trunk/packages/sift/trunk/debian/compat (rev 0)
+++ trunk/packages/sift/trunk/debian/compat 2012-02-17 21:35:37 UTC (rev 9700)
@@ -0,0 +1 @@
+7
Added: trunk/packages/sift/trunk/debian/control
===================================================================
--- trunk/packages/sift/trunk/debian/control (rev 0)
+++ trunk/packages/sift/trunk/debian/control 2012-02-17 21:35:37 UTC (rev 9700)
@@ -0,0 +1,18 @@
+Source: sift
+Section: science
+Priority: extra
+Maintainer: Laszlo Kajan <lkajan at rostlab.org>
+Build-Depends: debhelper (>= 7)
+Standards-Version: 3.9.1
+Homepage: http://blocks.fhcrc.org/sift/SIFT_help.html
+
+Package: sift
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}, csh
+Description: predicts if a substitution in a protein has a phenotypic effect
+ SIFT is a sequence homology-based tool that sorts intolerant from tolerant
+ amino acid substitutions and predicts whether an amino acid substitution
+ in a protein will have a phenotypic effect. SIFT is based on the premise
+ that protein evolution is correlated with protein function. Positions
+ important for function should be conserved in an alignment of the protein
+ family, whereas unimportant positions should appear diverse in an alignment.
Added: trunk/packages/sift/trunk/debian/copyright
===================================================================
--- trunk/packages/sift/trunk/debian/copyright (rev 0)
+++ trunk/packages/sift/trunk/debian/copyright 2012-02-17 21:35:37 UTC (rev 9700)
@@ -0,0 +1,139 @@
+This package was debianized by Laszlo Kajan <lkajan at rostlab.org> on
+Mon, 07 Dec 2009 15:22:27 +0100.
+
+It was downloaded from http://sift.jcvi.org/www/sift3.0.tar
+
+Upstream Author:
+
+ Pauline Ng <png at jcvi.org>
+
+Copyright:
+
+ (C) Copyright 1993-2008, Fred Hutchinson Cancer Research Center
+
+License:
+
+ ---------------------------------------------------------------------------
+ FHCRC NONCOMMERCIAL LICENSE
+ Fred Hutchinson Cancer Research Center
+ 1100 Fairview AV N
+ Seattle, WA 98109-1024
+
+
+ This license may be copied and distributed but may not be modified in
+ any way.
+
+ RECITALS:
+
+ A. Fred Hutchinson Cancer Research Center is a nonprofit
+ corporation dedicated to investigating the nature and causes of cancer
+ and methods of cancer prevention and treatment and for conducting
+ education in all phases of cancer research.
+
+ B. This license is designed to permit certain activities with
+ respect to any computer programs to which it applies on the terms
+ stated in this license.
+
+ TERMS AND CONDITIONS:
+
+ 1. Definitions.
+
+ "Program" means the computer software and associated
+ documentation in whatever form or format including source and object
+ code.
+
+ "Derivative Work" means any modification, addition, upgrade,
+ update or improvement of the Program and any other work constituting a
+ derivative work under the copyright laws.
+
+ "Licensee" means licensee of the Program under this license.
+
+ "FHCRC" means Fred Hutchinson Cancer Research Center.
+
+ 2. License, Copy, Distribute and Create Derivative Work. FHCRC
+ hereby grants Licensee and Licensee accepts, subject to the terms and
+ conditions of this Agreement, a nonexclusive, royalty-free license to
+ use, copy and sublicense the Program and prepare and sublicense
+ Derivative Works. This license is expressly limited as follows:
+
+ a. All copies of the Program must conspicuously show an
+ appropriate copyright notice and disclaimer of warranty and must
+ expressly refer to this license. In addition, Derivative Works must
+ conspicuously state that the Program has been modified and the date of
+ any modification.
+
+ b. Licensee may not charge any fee or royalty for copies
+ of the Program or Derivative Work. Licensee is authorized to
+ sublicense the Program and any Derivative Work to third parties on a
+ royalty-free basis subject to the terms of this license but may not
+ otherwise distribute the Program or any Derivative Work.
+ Notwithstanding the foregoing, Licensee may be reimbursed for any
+ actual expenses it incurs in reproducing or delivering a copy of the
+ Program or any Derivative Work.
+
+ c. This license does not apply to a work written entirely
+ by Licensee.
+
+ d. Licensee agrees to make available to any person to whom
+ it sublicenses this Program or a Derivative Work source code and
+ object code for the Program or Derivative Work.
+
+ e. Licensee may not impose any terms in addition to the
+ terms of this license on any third party to whom it distributes the
+ Program, any Derivative Work or any copy thereof.
+
+ 3. Reservation of Rights to FHCRC. FHCRC hereby reserves to
+ itself all rights of any nature whatsoever with respect to the
+ Program. Any Derivative Work created by FHCRC or its employees or
+ agents is not subject to the terms of this license.
+
+ 4. Termination of license. This license precludes any copying,
+ modification, sublicensing or other distribution of any Program or
+ Derivative Work except as expressly permitted under this license.
+ Violation of the terms of this license by Licensee will be deemed an
+ automatic termination of Licensee's rights under this license;
+ provided, however, that sublicenses derived from Licensee will remain
+ in full force and effect provided that any such sublicensees do not
+ breach the terms of this license.
+
+ 5. Acceptance of Terms of License. Licensee agrees that by
+ copying or distributing this Program or by creating, copying or
+ distributing any Derivative Work, Licensee has agreed to the terms of
+ this license.
+
+ 6. Limitation of Remedies and Indemnity. Because this Program
+ is licensed on a royalty-free basis, FHCRC and any person distributing
+ this Program or any Derivative Work expressly disclaim all warranties
+ express or implied including, without limitation, any implied warranty
+ of merchantability or fitness for a particular purpose. Neither FHCRC
+ nor any other party distributing the Program or any Derivative Work
+ will be liable for any damages arising from or related to the use of
+ the Program or such Derivative Work, including, without limitation,
+ incidental or consequential damages caused by the use or inability to
+ use the Program or loss or damage to data.
+
+ Licensee agrees to indemnify, defend and hold FHCRC harmless
+ from and against any claims, causes of action, damages, liabilities
+ and expenses, including without limitation attorney's fees, arising
+ from or related to Licensee's use, copying or distribution of the
+ Program or any Derivative Work.
+
+ 7. Severability. If any provision of this license is held
+ invalid under any applicable law or for any other reason, such
+ invalidity shall not effect any other provision of this license that
+ can be given effect without the invalid provision.
+
+ 8. Notice. Persons wishing to communicate with FHCRC
+ concerning this license or the Program should address their
+ communications as follows:
+
+ Fred Hutchinson Cancer Research Center
+ Attn: Dr. Steven Henikoff
+ 1100 Fairview AV N, A1-162
+ PO Box 19024
+ Seattle, WA 98109-1024
+
+ ---------------------------------------------------------------------------
+
+The Debian packaging is (C) 2009, Laszlo Kajan <lkajan at rostlab.org> and
+is licensed under the GPL, see `/usr/share/common-licenses/GPL'.
Added: trunk/packages/sift/trunk/debian/dirs
===================================================================
--- trunk/packages/sift/trunk/debian/dirs (rev 0)
+++ trunk/packages/sift/trunk/debian/dirs 2012-02-17 21:35:37 UTC (rev 9700)
@@ -0,0 +1 @@
+usr/bin
Added: trunk/packages/sift/trunk/debian/links
===================================================================
--- trunk/packages/sift/trunk/debian/links (rev 0)
+++ trunk/packages/sift/trunk/debian/links 2012-02-17 21:35:37 UTC (rev 9700)
@@ -0,0 +1 @@
+usr/bin/sift_for_submitting_fasta_seq.csh usr/bin/sift
Added: trunk/packages/sift/trunk/debian/rules
===================================================================
--- trunk/packages/sift/trunk/debian/rules (rev 0)
+++ trunk/packages/sift/trunk/debian/rules 2012-02-17 21:35:37 UTC (rev 9700)
@@ -0,0 +1,91 @@
+#!/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
+
+
+
+
+
+configure: configure-stamp
+configure-stamp:
+ dh_testdir
+ # Add here commands to configure the package.
+
+ touch configure-stamp
+
+
+build: build-stamp
+
+build-stamp: configure-stamp
+ dh_testdir
+
+ # Add here commands to compile the package.
+ $(MAKE) prefix=/usr
+ #docbook-to-man debian/sift.sgml > sift.1
+
+ touch $@
+
+clean:
+ dh_testdir
+ dh_testroot
+ rm -f build-stamp configure-stamp
+
+ # Add here commands to clean up after the build process.
+ $(MAKE) prefix=/usr distclean
+
+ dh_clean
+
+install: build
+ dh_testdir
+ dh_testroot
+ dh_prep
+ dh_installdirs
+
+ # Add here commands to install the package into debian/sift.
+ $(MAKE) DESTDIR=$(CURDIR)/debian/sift prefix=/usr install
+
+
+# Build architecture-independent files here.
+binary-indep: build install
+# We have nothing to do by default.
+
+# Build architecture-dependent files here.
+binary-arch: 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
+
+binary: binary-indep binary-arch
+.PHONY: build clean binary-indep binary-arch binary install configure
Property changes on: trunk/packages/sift/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
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