Author: tille Date: 2014-02-14 10:13:52 +0000 (Fri, 14 Feb 2014) New Revision: 16041
Added: trunk/packages/fish/ trunk/packages/fish/trunk/ trunk/packages/fish/trunk/debian/ trunk/packages/fish/trunk/debian/changelog trunk/packages/fish/trunk/debian/compat trunk/packages/fish/trunk/debian/control trunk/packages/fish/trunk/debian/copyright trunk/packages/fish/trunk/debian/fish-tests.README.Debian trunk/packages/fish/trunk/debian/fish-tests.install trunk/packages/fish/trunk/debian/fish.install trunk/packages/fish/trunk/debian/patches/ trunk/packages/fish/trunk/debian/patches/fix_makefile.patch trunk/packages/fish/trunk/debian/patches/series trunk/packages/fish/trunk/debian/rules trunk/packages/fish/trunk/debian/source/ trunk/packages/fish/trunk/debian/source/format trunk/packages/fish/trunk/debian/upstream trunk/packages/fish/trunk/debian/watch Log: Add initial packaging for fish Added: trunk/packages/fish/trunk/debian/changelog =================================================================== --- trunk/packages/fish/trunk/debian/changelog (rev 0) +++ trunk/packages/fish/trunk/debian/changelog 2014-02-14 10:13:52 UTC (rev 16041) @@ -0,0 +1,5 @@ +fish (1.0+dfsg-1) UNRELEASED; urgency=low + + * Initial release (Closes: #<bug>) + + -- Andreas Tille <[email protected]> Fri, 14 Feb 2014 09:23:04 +0100 Added: trunk/packages/fish/trunk/debian/compat =================================================================== --- trunk/packages/fish/trunk/debian/compat (rev 0) +++ trunk/packages/fish/trunk/debian/compat 2014-02-14 10:13:52 UTC (rev 16041) @@ -0,0 +1 @@ +9 Added: trunk/packages/fish/trunk/debian/control =================================================================== --- trunk/packages/fish/trunk/debian/control (rev 0) +++ trunk/packages/fish/trunk/debian/control 2014-02-14 10:13:52 UTC (rev 16041) @@ -0,0 +1,42 @@ +Source: fish +Section: science +Priority: optional +Maintainer: Debian Med Packaging Team <[email protected]> +Uploaders: Andreas Tille <[email protected]> +Build-Depends: debhelper (>= 9) +Standards-Version: 3.9.5 +Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/fish/trunk/ +Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/fish/trunk/ +Homepage: http://labs.bio.unc.edu/Vision/FISH/ + +Package: fish +Architecture: any +Depends: ${shlibs:Depends}, + ${misc:Depends} +Description: Fast Identification of Segmental Homology + FISH is software for identifying regions of common ancestry between + genome maps. Fast identification and statistical evaluation of + segmental homologies in comparative maps. + . + Development and maintenance of FISH is supported by funding from the + National Science Foundation (Plant Genome Research Program Grants + DBI-0110069 and DBI-0227314 to TJV and DMS-0102008 to PPC). + +Package: fish-tests +Architecture: all +Priority: extra +Enhances: fish +Depends: ${misc:Depends} +Suggests: fish +Description: Tests for Fast Identification of Segmental Homology (fish) + FISH is software for identifying regions of common ancestry between + genome maps. Fast identification and statistical evaluation of + segmental homologies in comparative maps. + . + Development and maintenance of FISH is supported by funding from the + National Science Foundation (Plant Genome Research Program Grants + DBI-0110069 and DBI-0227314 to TJV and DMS-0102008 to PPC). + . + This package contains the example data provided by upstream to enable + the user to test fish. + Added: trunk/packages/fish/trunk/debian/copyright =================================================================== --- trunk/packages/fish/trunk/debian/copyright (rev 0) +++ trunk/packages/fish/trunk/debian/copyright 2014-02-14 10:13:52 UTC (rev 16041) @@ -0,0 +1,184 @@ +Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: FISH +Upstream-Contact: Todd J. Vision <[email protected]> +Source: http://labs.bio.unc.edu/Vision/FISH/ +Files-Excluded: + bin + docs/fishmanual.ps + CVS + */CVS + */*/CVS + +Files: * +Copyright: 2003 University of North Carolina at Chapel Hill +License: LicenseAgreementFISH + As used herein, the term, "Program", below, refers to the source + code and the derivatives supplied by the authors, and a "work based on the + Program" means either the Program or any derivative work under copyright law: + that is to say, a work containing the Program or + a portion of it, either verbatim or with modifications and/or translated + into another language. (Hereinafter, translation is included without limitation + in the term "modification".) Each licensee is addressed as "you". + . + 1. SCOPE + Activities other than copying, distribution and modification are not + covered by this License; they are outside its scope. The act of running the + Program is not restricted, and the output from the Program is covered only + if its contents constitute a work based on the Program (independent of having + been made by running the Program). Whether that is true depends on what the + Program does. + . + 2. USER'S RIGHTS + You may copy and distribute verbatim copies of the Program's source code + as you receive it, in any medium, provided that you keep intact all the notices + that refer to this License and to the absence of any warranty; give any other + recipients of the Program a copy of this License along with the Program; + and conspicuously and appropriately publish on each copy a disclaimer of + warranty and the following statement: "Copyright ©2003, University of North + Carolina at Chapel Hill" If the code has been modified, you also may include + the following statement: "Modified by [your institution]." You may charge a + fee for the physical act of transferring a copy, and you may at your option + offer warranty protection in exchange for a fee. + . + 3. RIGHTS IN DERIVATIVE AND COMBINED WORKS + It is not the intent of this section to claim rights or contest + your rights to work written entirely by you; rather, the intent is to exercise + the right to control the distribution of derivative or collective works based + on the Program. Aggregation of another work not based on the Program + with the Program (or with a work based on the Program) on a volume of a storage + or distribution medium does not bring the other work under the scope of this + License. + . + You may modify your copy or copies of the Program or any portion of it, + thus forming a work based on the Program, and copy and distribute such modifications + or work under the terms of Section 2 above, provided that you also meet the following + conditions: + (a) You must cause the modified files to carry prominent notices stating that you + changed the files and the date and nature of any change. + (b) You must cause any work that you distribute or publish, that in whole + or in part contains or is derived from the Program or any part thereof, to be + licensed as a whole at no charge to all third parties under the terms of this License. + . + These requirements apply to the modified work as a whole. If identifiable + sections of that work are not derived from the Program, and can be reasonably + considered independent and separate works in themselves, then this License, + and its terms, do not apply to those sections when you distribute them as + separate works. But when you distribute the same sections as part of a whole + which is a work based on the Program, the distribution of the whole must + be on the terms of this License, whose permissions for other licensees extend + to the entire whole, and thus to each and every part regardless of who wrote + it. + . + 4. USER'S PROVISION AND/OR DISTRIBUTION OF SOURCE CODE + You may copy and distribute the Program (or a work based on it, under + Section 2) in object code or executable form under the terms of Sections + 1 and 2 above provided that you also accompany it with the complete corresponding + machine-readable source code, which must be distributed under the terms of + Sections 1 and 2 above on a medium customarily used for software interchange. + . + The source code for a work means the preferred form of the work for making + modifications to it. For an executable work, complete source code means all + the source code for all modules it contains, plus any associated interface + definition files, plus the scripts used to control compilation and installation + of the executable. However, as a special exception, the source code distributed + need not include anything that is normally distributed (in either source + or binary form) with the major components (compiler, kernel, and so on) of + the operating system on which the executable runs, unless that component + itself accompanies the executable. If distribution of executable or object code + is made by offering access to copy from a designated place, then offering + equivalent access to copy the source code from the same place counts as + distribution of the source code, even though third parties are not compelled + to copy the source along with the object code. + . + 5. LICENSE RESTRICTIONS + (a) You may not copy, modify, sublicense, or distribute the Program + except as expressly provided under this License. Any attempt otherwise to + copy, modify, sublicense or distribute the Program is void, and will automatically + terminate your rights under this License. However, parties who have received + copies, or rights, from you under this License will not have their licenses + terminated so long as such parties remain in full compliance. + (b) You are not required to accept this License, since you have not + signed it. However, nothing else grants you permission to modify or distribute + the Program or its derivative works. These actions are prohibited by law + if you do not accept this License. Therefore, by modifying or distributing + the Program (or any work based on the Program), you indicate your acceptance + of this License to do so, and all its terms and conditions for copying, distributing + or modifying the Program or works based on it. + (c) If, as a consequence of a court judgment or allegation of patent + infringement or for any other reason (not limited to patent issues), conditions + are imposed on you (whether by court order, agreement or otherwise) that + contradict the conditions of this License, they do not excuse you from the + conditions of this License. If you cannot distribute so as to satisfy simultaneously + your obligations under this License and any other pertinent obligations, + then as a consequence you may not distribute the Program at all. For example, + if a patent license would not permit royalty-free redistribution of the Program + by all those who receive copies directly or indirectly through you, then + the only way you could satisfy both it and this License would be to refrain + entirely from distribution of the Program. + . + It is not the purpose of this section to induce you to infringe any patents + or other property right claims or to contest validity of any such claims; + this section has the sole purpose of protecting the integrity of the free + software distribution system, which is implemented by public license practices. + Many people have made generous contributions to the wide range of software + distributed through that system in reliance on consistent application of + that system; it is up to the author/donor to decide if he or she is willing + to distribute software through any other system and a licensee cannot impose + that choice. + . + 6. LICENSE CONVEYS TO SUBSEQUENT RECIPIENTS + Each time you redistribute the Program (or any work based on the Program), + the recipient automatically receives a license from the original licensor + to copy, distribute or modify the Program subject to these terms and conditions. + You may not impose any further restrictions on the recipients' exercise of + the rights granted herein. You are not responsible for enforcing compliance + by third parties to this License. + . + 7. SEVERABILITY + If any portion of this license or any portion of any section of this + license is held invalid or unenforceable under any particular circumstance, + the balance of the section is intended to apply and the section as a whole + is intended to apply in other circumstances. + . + 8. NO WARRANTY + BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY + FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE + STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE + PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, + INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY + AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND + PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, + YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION. + . + IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING + WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE + THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY + GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE + USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF + DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD + PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), + EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF + SUCH DAMAGES. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY + FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE + STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE + PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, + INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY + AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND + PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, + YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION. + . + IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING + WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE + THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY + GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE + USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF + DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD + PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), + EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF + SUCH DAMAGES. + +Files: debian/* +Copyright: 2014 Andreas Tille <[email protected]> +License: GPLv3+ + The full text of GPL license version 3 can be found at + /usr/share/common-licenses/GPL-3 . Added: trunk/packages/fish/trunk/debian/fish-tests.README.Debian =================================================================== --- trunk/packages/fish/trunk/debian/fish-tests.README.Debian (rev 0) +++ trunk/packages/fish/trunk/debian/fish-tests.README.Debian 2014-02-14 10:13:52 UTC (rev 16041) @@ -0,0 +1,9 @@ +Test data for package fish +========================== + +The data are installed at + + /var/lib/fish + +See the file SAMPLE.txt there for more instructions. + Added: trunk/packages/fish/trunk/debian/fish-tests.install =================================================================== --- trunk/packages/fish/trunk/debian/fish-tests.install (rev 0) +++ trunk/packages/fish/trunk/debian/fish-tests.install 2014-02-14 10:13:52 UTC (rev 16041) @@ -0,0 +1,2 @@ +SAMPLES.txt var/lib/fish +sample_* var/lib/fish Added: trunk/packages/fish/trunk/debian/fish.install =================================================================== --- trunk/packages/fish/trunk/debian/fish.install (rev 0) +++ trunk/packages/fish/trunk/debian/fish.install 2014-02-14 10:13:52 UTC (rev 16041) @@ -0,0 +1 @@ +src/fish usr/bin Added: trunk/packages/fish/trunk/debian/patches/fix_makefile.patch =================================================================== --- trunk/packages/fish/trunk/debian/patches/fix_makefile.patch (rev 0) +++ trunk/packages/fish/trunk/debian/patches/fix_makefile.patch 2014-02-14 10:13:52 UTC (rev 16041) @@ -0,0 +1,26 @@ +Author: Andreas Tille <[email protected]> +Last-Changed: Fri, 14 Feb 2014 09:23:04 +0100 +Description: Fix very basic makefile + - Fix clean target + - propagate build options + +--- a/makefile ++++ b/makefile +@@ -3,14 +3,14 @@ CC = g++ -ggdb + + + all : realall +- make bin ++ # make bin + + realall : +- (cd ./src; $(CC) -c point.cpp; $(CC) fish.cpp point.o -o fish) ++ (cd ./src; $(CC) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) point.cpp fish.cpp -o fish) + + bin : + mkdir bin + mv src/fish ./bin + clean : +- (cd src ; rm *.o) ++ (cd src ; rm -f *.o) + (rm -rf ./bin) Added: trunk/packages/fish/trunk/debian/patches/series =================================================================== --- trunk/packages/fish/trunk/debian/patches/series (rev 0) +++ trunk/packages/fish/trunk/debian/patches/series 2014-02-14 10:13:52 UTC (rev 16041) @@ -0,0 +1 @@ +fix_makefile.patch Added: trunk/packages/fish/trunk/debian/rules =================================================================== --- trunk/packages/fish/trunk/debian/rules (rev 0) +++ trunk/packages/fish/trunk/debian/rules 2014-02-14 10:13:52 UTC (rev 16041) @@ -0,0 +1,23 @@ +#!/usr/bin/make -f + +# DH_VERBOSE := 1 + +# some helpful variables - uncomment them if needed +# shamelessly stolen from http://jmtd.net/log/awk/ +#DEBVERS := $(shell dpkg-parsechangelog | awk '/^Version:/ {print $$2}') +#VERSION := $(shell echo '$(DEBVERS)' | sed -e 's/^[0-9]*://' -e 's/-.*//') +#DEBFLAVOR := $(shell dpkg-parsechangelog | awk '/^Distribution:/ {print $$2}') +#DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}') +#DEBIAN_BRANCH := $(shell awk 'BEGIN{FS="[= ]+"} /debian-branch/ {print $$2}' debian/gbp.conf) +#GIT_TAG := $(subst ~,_,$(VERSION)) + +# alternatively to manually set those variables you can +# include /usr/share/cdbs/1/rules/buildvars.mk +# and use what is set there. Any hint whether dh might set variables in +# a similar manner are welcome. + +%: + dh $@ + +#get-orig-source: +# . debian/get-orig-source Property changes on: trunk/packages/fish/trunk/debian/rules ___________________________________________________________________ Added: svn:executable + * Added: trunk/packages/fish/trunk/debian/source/format =================================================================== --- trunk/packages/fish/trunk/debian/source/format (rev 0) +++ trunk/packages/fish/trunk/debian/source/format 2014-02-14 10:13:52 UTC (rev 16041) @@ -0,0 +1 @@ +3.0 (quilt) Added: trunk/packages/fish/trunk/debian/upstream =================================================================== --- trunk/packages/fish/trunk/debian/upstream (rev 0) +++ trunk/packages/fish/trunk/debian/upstream 2014-02-14 10:13:52 UTC (rev 16041) @@ -0,0 +1,12 @@ +Reference: + Author: Peter P. Calabrese and Sugata Chakravarty and Todd J. Vision + Title: Fast identification and statistical evaluation of segmental homologies in comparative maps + Journal: Bioinformatics + Year: 2003 + Volume: 19 + Number: Suppl 1 + Pages: i74-i80 + DOI: 10.1093/bioinformatics/btg1008 + PMID: 12855440 + URL: http://bioinformatics.oxfordjournals.org/content/19/suppl_1/i74 + eprint: http://bioinformatics.oxfordjournals.org/content/19/suppl_1/i74.full.pdf+html Added: trunk/packages/fish/trunk/debian/watch =================================================================== --- trunk/packages/fish/trunk/debian/watch (rev 0) +++ trunk/packages/fish/trunk/debian/watch 2014-02-14 10:13:52 UTC (rev 16041) @@ -0,0 +1,3 @@ +version=3 +opts=dversionmangle=s/\+dfsg// \ + http://labs.bio.unc.edu/Vision/FISH/ .*/vision/lab/FISH/FISH-([\d.]+)-src\.tar\.z _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
