[med-svn] [piler] 02/02: piler (0~20140707-1) unstable; urgency=low
Afif Elghraoui
afif-guest at moszumanska.debian.org
Fri Nov 20 07:14:13 UTC 2015
This is an automated email from the git hooks/post-receive script.
afif-guest pushed a commit to branch master
in repository piler.
commit b703b30d46a846128399610eafde605d36e0794a
Author: Afif Elghraoui <afif at ghraoui.name>
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 <afif at ghraoui.name> 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 <debian-med-packaging at lists.alioth.debian.org>
+Uploaders:
+ Afif Elghraoui <afif at ghraoui.name>,
+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 <bob at drive5.com>
+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 <afif at ghraoui.name>
+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 <afif at ghraoui.name>
+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 <afif at ghraoui.name>,
+.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
--
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