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 <[email protected]> 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 <[email protected]> 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 <[email protected]> +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 <[email protected]> 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 <[email protected]> + +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 <[email protected]> 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 + * _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
