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commit b703b30d46a846128399610eafde605d36e0794a Author: Afif Elghraoui <[email protected]> Date: Thu Nov 19 23:12:48 2015 -0800 piler (0~20140707-1) unstable; urgency=low * Initial release (Closes: #805607) --- debian/changelog | 5 +++++ debian/compat | 1 + debian/control | 25 +++++++++++++++++++++++++ debian/copyright | 37 +++++++++++++++++++++++++++++++++++++ debian/install | 2 ++ debian/manpages | 1 + debian/patches/compiler-flags.patch | 27 +++++++++++++++++++++++++++ debian/patches/series | 1 + debian/piler2.1 | 11 +++++++++++ debian/rules | 10 ++++++++++ debian/source/format | 1 + debian/upstream/metadata | 12 ++++++++++++ debian/watch | 3 +++ 13 files changed, 136 insertions(+) diff --git a/debian/changelog b/debian/changelog new file mode 100644 index 0000000..ee229ef --- /dev/null +++ b/debian/changelog @@ -0,0 +1,5 @@ +piler (0~20140707-1) unstable; urgency=low + + * Initial release (Closes: #805607) + + -- Afif Elghraoui <[email protected]> Thu, 19 Nov 2015 20:36:40 -0800 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..5a32d90 --- /dev/null +++ b/debian/control @@ -0,0 +1,25 @@ +Source: piler +Section: science +Priority: optional +Maintainer: Debian Med Packaging Team <[email protected]> +Uploaders: + Afif Elghraoui <[email protected]>, +Build-Depends: + debhelper (>= 9), +Standards-Version: 3.9.6 +Homepage: http://www.drive5.com/piler/ +Vcs-Git: git://anonscm.debian.org/debian-med/piler.git +Vcs-Browser: http://anonscm.debian.org/cgit/debian-med/piler.git + +Package: piler +Architecture: any +Depends: + ${shlibs:Depends}, + ${misc:Depends}, +Recommends: + muscle, +Description: genomic repeat analysis + PILER (Parsimonious Inference of a Library of Elementary Repeats) + searches a genome sequence for repetitive elements. It implements search + algorithms that identify characteristic patterns of local alignments + induced by certain classes of repeats. diff --git a/debian/copyright b/debian/copyright new file mode 100644 index 0000000..51e909b --- /dev/null +++ b/debian/copyright @@ -0,0 +1,37 @@ +Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: piler +Upstream-Contact: Robert Edgar <[email protected]> +Source: http://www.drive5.com/piler/ + +Files: * +Copyright: Robert Edgar +License: PublicDomain + The PILER software, including object and source code and documentation, is + here by donated to the public domain. + . + Disclaimer of warranty + THIS SOFTWARE IS PROVIDED "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESS + OR IMPLIED, INCLUDING WITHOUT LIMITATION IMPLIED WARRANTIES OF MERCHANTABILITY + AND FITNESS FOR A PARTICULAR PURPOSE. +Comment: + The public domain declaration is found on the project homepage. The text + above is on the page http://www.drive5.com/piler/license.htm + +Files: debian/* +Copyright: 2015 Afif Elghraoui <[email protected]> +License: GPL-2+ + This package is free software; you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation; either version 2 of the License, or + (at your option) any later version. + . + This package is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + . + You should have received a copy of the GNU General Public License + along with this program. If not, see <http://www.gnu.org/licenses/> + . + On Debian systems, the complete text of the GNU General + Public License version 2 can be found in "/usr/share/common-licenses/GPL-2". diff --git a/debian/install b/debian/install new file mode 100644 index 0000000..97713ff --- /dev/null +++ b/debian/install @@ -0,0 +1,2 @@ +piler2 usr/bin + diff --git a/debian/manpages b/debian/manpages new file mode 100644 index 0000000..4fef4ae --- /dev/null +++ b/debian/manpages @@ -0,0 +1 @@ +debian/piler2.1 diff --git a/debian/patches/compiler-flags.patch b/debian/patches/compiler-flags.patch new file mode 100644 index 0000000..8c65d83 --- /dev/null +++ b/debian/patches/compiler-flags.patch @@ -0,0 +1,27 @@ +Description: Allow compiler flags to be passed to build +Author: Afif Elghraoui <[email protected]> +Forwarded: no +Last-Update: 2015-11-19 +--- piler.orig/Makefile ++++ piler/Makefile +@@ -1,5 +1,5 @@ +-CFLAGS = -O3 -DNDEBUG=1 +-LDLIBS = -lm -static ++CFLAGS += -O3 -DNDEBUG=1 ++LDLIBS = $(LDFLAGS) -lm + # LDLIBS = -lm + + OBJ = .o +@@ -8,10 +8,10 @@ + RM = rm -f + CP = cp + +-GPP = g++ ++GPP = $(CXX) + LD = $(GPP) $(CFLAGS) + CPP = $(GPP) -c $(CFLAGS) +-CC = gcc -c $(CFLAGS) ++CC := $(CC) -c $(CFLAGS) + + all: piler2 + diff --git a/debian/patches/series b/debian/patches/series new file mode 100644 index 0000000..a4675fc --- /dev/null +++ b/debian/patches/series @@ -0,0 +1 @@ +compiler-flags.patch diff --git a/debian/piler2.1 b/debian/piler2.1 new file mode 100644 index 0000000..2ee13e1 --- /dev/null +++ b/debian/piler2.1 @@ -0,0 +1,11 @@ +.\" (C) Copyright 2015 Afif Elghraoui <[email protected]>, +.TH PILER2 1 "November 2015" +.SH NAME +piler2 \- search a genomic sequence for repeats +.SH SYNOPSIS +.B piler2 +.RI [ options ] " files" ... +.SH DESCRIPTION +Please see the user guide (linked below) for usage instructions. +.SH SEE ALSO +http://www.drive5.com/piler/piler_userguide.html diff --git a/debian/rules b/debian/rules new file mode 100755 index 0000000..0e79883 --- /dev/null +++ b/debian/rules @@ -0,0 +1,10 @@ +#!/usr/bin/make -f + +#DH_VERBOSE = 1 + +include /usr/share/dpkg/default.mk + +export CFLAGS := $(CPPFLAGS) $(CFLAGS) + +%: + dh $@ --parallel 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/metadata b/debian/upstream/metadata new file mode 100644 index 0000000..0223e4c --- /dev/null +++ b/debian/upstream/metadata @@ -0,0 +1,12 @@ +Reference: + Author: Robert C. Edgar and Eugene W. Myers + Title: "PILER: identification and classification of genomic repeats" + Journal: Bioinformatics + Year: 2005 + Volume: 21 + Number: suppl 1 + Pages: i152-i158 + DOI: 10.1093/bioinformatics/bti1003 + PMID: 15961452 + URL: http://bioinformatics.oxfordjournals.org/content/21/suppl_1/i152.short + eprint: http://bioinformatics.oxfordjournals.org/content/21/suppl_1/i152.full.pdf+html diff --git a/debian/watch b/debian/watch new file mode 100644 index 0000000..300fef7 --- /dev/null +++ b/debian/watch @@ -0,0 +1,3 @@ +version=3 + +# There is nothing for the watch file to target -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/piler.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
