[med-svn] [unc-fish] 01/12: Add initial packaging for fish
Andreas Tille
tille at debian.org
Fri Dec 29 21:41:58 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository unc-fish.
commit 276e1695a02beebf4d6099ceb32240b4b0caf029
Author: Andreas Tille <tille at debian.org>
Date: Fri Feb 14 10:13:52 2014 +0000
Add initial packaging for fish
---
debian/changelog | 5 ++
debian/compat | 1 +
debian/control | 42 +++++++++
debian/copyright | 184 ++++++++++++++++++++++++++++++++++++++
debian/fish-tests.README.Debian | 9 ++
debian/fish-tests.install | 2 +
debian/fish.install | 1 +
debian/patches/fix_makefile.patch | 26 ++++++
debian/patches/series | 1 +
debian/rules | 23 +++++
debian/source/format | 1 +
debian/upstream | 12 +++
debian/watch | 3 +
13 files changed, 310 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..93a403c
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+fish (1.0+dfsg-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org> Fri, 14 Feb 2014 09:23:04 +0100
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..ec63514
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+9
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..9088deb
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,42 @@
+Source: fish
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
+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.
+
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..76e82b1
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,184 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: FISH
+Upstream-Contact: Todd J. Vision <tjv at bio.unc.edu>
+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 <tille at debian.org>
+License: GPLv3+
+ The full text of GPL license version 3 can be found at
+ /usr/share/common-licenses/GPL-3 .
diff --git a/debian/fish-tests.README.Debian b/debian/fish-tests.README.Debian
new file mode 100644
index 0000000..7a5d1a5
--- /dev/null
+++ b/debian/fish-tests.README.Debian
@@ -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.
+
diff --git a/debian/fish-tests.install b/debian/fish-tests.install
new file mode 100644
index 0000000..0109b08
--- /dev/null
+++ b/debian/fish-tests.install
@@ -0,0 +1,2 @@
+SAMPLES.txt var/lib/fish
+sample_* var/lib/fish
diff --git a/debian/fish.install b/debian/fish.install
new file mode 100644
index 0000000..777eb37
--- /dev/null
+++ b/debian/fish.install
@@ -0,0 +1 @@
+src/fish usr/bin
diff --git a/debian/patches/fix_makefile.patch b/debian/patches/fix_makefile.patch
new file mode 100644
index 0000000..e3c58c5
--- /dev/null
+++ b/debian/patches/fix_makefile.patch
@@ -0,0 +1,26 @@
+Author: Andreas Tille <tille at debian.org>
+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)
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..1d3db58
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+fix_makefile.patch
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..58ec00b
--- /dev/null
+++ b/debian/rules
@@ -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
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)
diff --git a/debian/upstream b/debian/upstream
new file mode 100644
index 0000000..1617605
--- /dev/null
+++ b/debian/upstream
@@ -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
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..1c1cd5c
--- /dev/null
+++ b/debian/watch
@@ -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
--
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