Author: plessy Date: 2009-08-25 11:30:08 +0000 (Tue, 25 Aug 2009) New Revision: 3820
Added: trunk/packages/srf/trunk/debian/README.source trunk/packages/srf/trunk/debian/libsrf-dev.install trunk/packages/srf/trunk/debian/srf-doc.doc-base Removed: trunk/packages/srf/trunk/debian/README.Debian trunk/packages/srf/trunk/debian/docs trunk/packages/srf/trunk/debian/srf.doc-base Modified: trunk/packages/srf/trunk/debian/changelog trunk/packages/srf/trunk/debian/control trunk/packages/srf/trunk/debian/copyright trunk/packages/srf/trunk/debian/rules trunk/packages/srf/trunk/debian/srf-doc.docs Log: Added the latest version of the spec, and finished packaging. Deleted: trunk/packages/srf/trunk/debian/README.Debian =================================================================== --- trunk/packages/srf/trunk/debian/README.Debian 2009-08-25 10:05:38 UTC (rev 3819) +++ trunk/packages/srf/trunk/debian/README.Debian 2009-08-25 11:30:08 UTC (rev 3820) @@ -1,6 +0,0 @@ -srf for Debian --------------- - -<possible notes regarding this package - if none, delete this file> - - -- Charles Plessy <[email protected]> Mon, 07 Jul 2008 19:06:55 +0900 Added: trunk/packages/srf/trunk/debian/README.source =================================================================== --- trunk/packages/srf/trunk/debian/README.source (rev 0) +++ trunk/packages/srf/trunk/debian/README.source 2009-08-25 11:30:08 UTC (rev 3820) @@ -0,0 +1,16 @@ +I have added the latest version of the SRF specification to this package: + + - SRF_v_1_3_2_June_19th_2008-0001.pdf was downloaded from the archives of the + Ssrformat mailing list (http://www.bcgsc.ca/pipermail/ssrformat/2008-September/000554.html). + + - SRF_v_1_3_2_June_19th_2008.doc was communicated to me by Asim Siddiqui. + +Since SRF_v_1_3_2_June_19th_2008.doc is the latest version, I beleive that this +makes effectively free the PDF file SequenceReadFormat_v_1_3_1_Feb_27th_08.pdf, +whose sources were not available in the original upstream archive. + +In addition, the Debian binary packages are produced after applying patches to +the original sources. For more instruction about how to manage the patches, +please refer to the file ‘/usr/share/doc/quilt/README.source’. + + -- Charles Plessy <[email protected]> Tue, 25 Aug 2009 19:36:31 +0900 Modified: trunk/packages/srf/trunk/debian/changelog =================================================================== --- trunk/packages/srf/trunk/debian/changelog 2009-08-25 10:05:38 UTC (rev 3819) +++ trunk/packages/srf/trunk/debian/changelog 2009-08-25 11:30:08 UTC (rev 3820) @@ -1,4 +1,4 @@ -srf (0.1-1) UNRELEASED; urgency=low +srf (0.1+dfsg-1) UNRELEASED; urgency=low * Initial release (Closes: #489983) Modified: trunk/packages/srf/trunk/debian/control =================================================================== --- trunk/packages/srf/trunk/debian/control 2009-08-25 10:05:38 UTC (rev 3819) +++ trunk/packages/srf/trunk/debian/control 2009-08-25 11:30:08 UTC (rev 3820) @@ -1,23 +1,18 @@ Source: srf Section: science Priority: optional -Maintainer: Debian-Med Packaging Team <[email protected]> +Maintainer: Debian Med Packaging Team <[email protected]> DM-Upload-Allowed: yes Uploaders: Charles Plessy <[email protected]> Build-Depends: cdbs, quilt, debhelper (>= 7), autotools-dev, libcurl4-gnutls-dev, libstaden-read-dev -Standards-Version: 3.8.0 +Standards-Version: 3.8.3 Homepage: http://srf.sourceforge.net/ Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/srf/trunk/?rev=0&sc=0 Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/srf/trunk/ -Package: srf -Architecture: any -Depends: ${shlibs:Depends}, ${misc:Depends} -Description: <insert up to 60 chars description> - <insert long description, indented with spaces> - Package: srf-doc Architecture: all +Section: doc Depends: ${misc:Depends} Description: specification documents for the SRF format DNA sequence data SRF (sort for Sequence Read Format) is a generic format capable of storing @@ -28,11 +23,11 @@ formats to reference reads without duplication of all of the read specific information. . - This package contains the version 1.3 and the draft of the version - 1.3.1 of the SRF specification. + This package contains the version 1.3.2 of the specification. -Package: libsrf1 +Package: libsrf-dev Architecture: any +Section: libdevel Depends: ${shlibs:Depends}, ${misc:Depends} Description: C++ implementation of the SRF format for DNA sequence data SRF (sort for Sequence Read Format) is a generic format capable of storing Modified: trunk/packages/srf/trunk/debian/copyright =================================================================== --- trunk/packages/srf/trunk/debian/copyright 2009-08-25 10:05:38 UTC (rev 3819) +++ trunk/packages/srf/trunk/debian/copyright 2009-08-25 11:30:08 UTC (rev 3820) @@ -4,9 +4,11 @@ Contact : http://www.bcgsc.ca/mailman/listinfo/ssrformat Source : http://downloads.sourceforge.net/project/srf/srf/v0.1/srf-v0.1.tar.gz + Copyright : 2007, Asim Siddiqui License : Apache-2.0 + Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at @@ -19,5 +21,43 @@ See the License for the specific language governing permissions and limitations under the License. + On Debian systems, the complete text of the Apache license version 2 is distributed in the file ’/usr/share/common-licenses/Apache-2.0’. + + +File : src/SRF_util.cc +Copyright : Genome Research Ltd (GRL). +License : GRL + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + * Redistributions of source code must retain the above copyright + notice, this list of conditions and the following disclaimer. + + * Redistributions in binary form must reproduce the above + copyright notice, this list of conditions and the following + disclaimer in the documentation and/or other materials + provided with the distribution. + + * Neither the name of the Genome Research Limited nor the + names of its contributors may be used to endorse or promote + products derived from this software without specific prior + written permission. + + THIS SOFTWARE IS PROVIDED BY GRL ``AS IS'' AND ANY EXPRESS OR + IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE + ARE DISCLAIMED. IN NO EVENT SHALL GRL BE LIABLE FOR ANY DIRECT, + INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR + SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) + HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, + STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) + ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED + OF THE POSSIBILITY OF SUCH DAMAGE. + +The upstream autor of src/SRF_util.cc confirmed in a private email that the +current license the original program where it was taken from, the Staden +io-lib, applies instead of the non-free statement contained in the file itself. Deleted: trunk/packages/srf/trunk/debian/docs =================================================================== --- trunk/packages/srf/trunk/debian/docs 2009-08-25 10:05:38 UTC (rev 3819) +++ trunk/packages/srf/trunk/debian/docs 2009-08-25 11:30:08 UTC (rev 3820) @@ -1 +0,0 @@ -README Added: trunk/packages/srf/trunk/debian/libsrf-dev.install =================================================================== --- trunk/packages/srf/trunk/debian/libsrf-dev.install (rev 0) +++ trunk/packages/srf/trunk/debian/libsrf-dev.install 2009-08-25 11:30:08 UTC (rev 3820) @@ -0,0 +1 @@ +src/libsrf.a usr/lib Modified: trunk/packages/srf/trunk/debian/rules =================================================================== --- trunk/packages/srf/trunk/debian/rules 2009-08-25 10:05:38 UTC (rev 3819) +++ trunk/packages/srf/trunk/debian/rules 2009-08-25 11:30:08 UTC (rev 3820) @@ -1,9 +1,7 @@ #!/usr/bin/make -f +DEB_COMPRESS_EXCLUDE = .pdf + include /usr/share/cdbs/1/rules/patchsys-quilt.mk include /usr/share/cdbs/1/rules/debhelper.mk include /usr/share/cdbs/1/class/autotools.mk - -#CXXFLAGS += -I/usr/include/io_lib - -# Add here any variable or target overrides you need. Copied: trunk/packages/srf/trunk/debian/srf-doc.doc-base (from rev 3819, trunk/packages/srf/trunk/debian/srf.doc-base) =================================================================== --- trunk/packages/srf/trunk/debian/srf-doc.doc-base (rev 0) +++ trunk/packages/srf/trunk/debian/srf-doc.doc-base 2009-08-25 11:30:08 UTC (rev 3820) @@ -0,0 +1,10 @@ +Document: srf +Title: SRF specification version 1.3.2 +Author: This format has been developed as an open collaborative effort between many groups and individuals (see inside). +Abstract: + This document describes a machine and technology independent format for storing + DNA sequence data and associated quality values. +Section: Science/Biology + +Format: PDF +Files: /usr/share/doc/srf-doc/SRF_v_1_3_2_June_19th_2008-0001.pdf Modified: trunk/packages/srf/trunk/debian/srf-doc.docs =================================================================== --- trunk/packages/srf/trunk/debian/srf-doc.docs 2009-08-25 10:05:38 UTC (rev 3819) +++ trunk/packages/srf/trunk/debian/srf-doc.docs 2009-08-25 11:30:08 UTC (rev 3820) @@ -1,4 +1,2 @@ -docs/SequenceReadFormat_v_1_3_1_Feb_27th_08.pdf -docs/ShortSequenceFormatDec18th_v_1_3.doc -docs/ShortSequenceFormatDec18th_v_1_3.pdf -docs/ShortSequenceFormatFeb11th_v1_approved.doc +README +docs/SRF_v_1_3_2_June_19th_2008-0001.pdf Deleted: trunk/packages/srf/trunk/debian/srf.doc-base =================================================================== --- trunk/packages/srf/trunk/debian/srf.doc-base 2009-08-25 10:05:38 UTC (rev 3819) +++ trunk/packages/srf/trunk/debian/srf.doc-base 2009-08-25 11:30:08 UTC (rev 3820) @@ -1,22 +0,0 @@ -Document: srf -Title: Debian srf Manual -Author: <insert document author here> -Abstract: This manual describes what srf is - and how it can be used to - manage online manuals on Debian systems. -Section: unknown - -Format: debiandoc-sgml -Files: /usr/share/doc/srf/srf.sgml.gz - -Format: postscript -Files: /usr/share/doc/srf/srf.ps.gz - -Format: text -Files: /usr/share/doc/srf/srf.text.gz - -Format: HTML -Index: /usr/share/doc/srf/html/index.html -Files: /usr/share/doc/srf/html/*.html - - _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
