[med-svn] [codonw] 02/03: add debian directory
Sascha Steinbiss
sascha-guest at moszumanska.debian.org
Fri Nov 20 23:17:19 UTC 2015
This is an automated email from the git hooks/post-receive script.
sascha-guest pushed a commit to branch master
in repository codonw.
commit e8556a25a4dd35dee76558c147f3f77d46105ab8
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date: Fri Nov 20 23:02:27 2015 +0000
add debian directory
---
debian/changelog | 5 ++++
debian/compat | 1 +
debian/control | 23 ++++++++++++++++
debian/copyright | 30 ++++++++++++++++++++
debian/get-orig-source | 45 ++++++++++++++++++++++++++++++
debian/install | 1 +
debian/links | 18 ++++++++++++
debian/manpages | 1 +
debian/patches/define_linux | 12 ++++++++
debian/patches/enable_clean | 30 ++++++++++++++++++++
debian/patches/hardening | 62 ++++++++++++++++++++++++++++++++++++++++++
debian/patches/hardening.patch | 54 ++++++++++++++++++++++++++++++++++++
debian/patches/remove_pause | 27 ++++++++++++++++++
debian/patches/series | 4 +++
debian/rules | 26 ++++++++++++++++++
debian/source/format | 1 +
debian/watch | 3 ++
17 files changed, 343 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..d4ad308
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+codonw (1.4.4-1) unstable; urgency=low
+
+ * Initial release (Closes: #<bug>)
+
+ -- Sascha Steinbiss <sascha at steinbiss.name> Fri, 20 Nov 2015 21:24:47 +0000
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..8dff573
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,23 @@
+Source: codonw
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Sascha Steinbiss <sascha at steinbiss.name>
+Build-Depends: debhelper (>= 9)
+Standards-Version: 3.9.6
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/<pkg>/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/<pkg>/trunk/
+Homepage: http://codonw.sourceforge.net
+
+Package: codonw
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: Correspondence Analysis of Codon Usage
+ CodonW is a package for codon usage analysis. It was designed to simplify
+ Multivariate Analysis (MVA) of codon usage. The MVA method employed in
+ CodonW is correspondence analysis (COA) (the most popular MVA method for
+ codon usage analysis). CodonW can generate a COA for codon usage, relative
+ synonymous codon usage or amino acid usage. Additional analyses of codon
+ usage include investigation of optimal codons, codon and dinucleotide bias,
+ and/or base composition. CodonW analyses sequences encoded by genetic codes
+ other than the universal code.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..32edf2f
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,30 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: codonw
+Source: http://sourceforge.net/projects/codonw/
+Files-Excluded: CVS
+
+Files: *
+Copyright: © 2005 John F. Peden <jfp%23hanson-codonw at yahoo.com>
+License: GPL-2
+
+Files: debian/*
+Copyright: © 2015 Sascha Steinbiss <sascha at steinbiss.name>
+License: GPL-2
+
+License: GPL-2
+ This program 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 program 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, write to the Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ .
+ On Debian systems you can find the full test of the GNU General Public
+ License version 2 at /usr/share/common-licenses/GPL-2.
\ No newline at end of file
diff --git a/debian/get-orig-source b/debian/get-orig-source
new file mode 100755
index 0000000..e486809
--- /dev/null
+++ b/debian/get-orig-source
@@ -0,0 +1,45 @@
+#!/bin/sh
+# if you need to repack for whatever reason you can
+# use this script via uscan or directly
+#
+# FIXME: currently the code is not conform to Debian Policy
+# http://www.debian.org/doc/debian-policy/ch-source.html
+# "get-orig-source (optional)"
+# This target may be invoked in any directory, ...
+# --> currently it is assumed the script is called in the
+# source directory featuring the debian/ dir
+
+COMPRESS=xz
+
+set -e
+NAME=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
+
+if ! echo $@ | grep -q upstream-version ; then
+ VERSION=`dpkg-parsechangelog | awk '/^Version:/ { print $2 }' | sed 's/\([0-9\.]\+\)-[0-9]\+$/\1/'`
+ uscan --force-download
+else
+ VERSION=`echo $@ | sed "s?^.*--upstream-version \([0-9.]\+\) .*${NAME}.*?\1?"`
+ if echo "$VERSION" | grep -q "upstream-version" ; then
+ echo "Unable to parse version number"
+ exit
+ fi
+fi
+
+TARDIR=${NAME}-${VERSION}
+mkdir -p ../tarballs
+cd ../tarballs
+# need to clean up the tarballs dir first because upstream tarball might
+# contain a directory with unpredictable name
+rm -rf *
+tar -xaf ../${TARDIR}.tar.gz
+
+UPSTREAMTARDIR=`find . -mindepth 1 -maxdepth 1 -type d`
+if [ "${UPSTREAMTARDIR}" != "${TARDIR}" ] ; then
+ mv "${UPSTREAMTARDIR}" "${TARDIR}"
+fi
+
+# Remove useless binaries
+# ... do something which needs to be done ...
+
+GZIP="--best --no-name" tar --owner=root --group=root --mode=a+rX -caf "$NAME"_"$VERSION".orig.tar.${COMPRESS} "${TARDIR}"
+rm -rf ${TARDIR}
diff --git a/debian/install b/debian/install
new file mode 100644
index 0000000..d478118
--- /dev/null
+++ b/debian/install
@@ -0,0 +1 @@
+codonw /usr/bin
\ No newline at end of file
diff --git a/debian/links b/debian/links
new file mode 100644
index 0000000..bba9228
--- /dev/null
+++ b/debian/links
@@ -0,0 +1,18 @@
+/usr/bin/codonw /usr/bin/rscu
+/usr/bin/codonw /usr/bin/cu
+/usr/bin/codonw /usr/bin/aau
+/usr/bin/codonw /usr/bin/raau
+/usr/bin/codonw /usr/bin/tidy
+/usr/bin/codonw /usr/bin/reader
+/usr/bin/codonw /usr/bin/cutab
+/usr/bin/codonw /usr/bin/cutot
+/usr/bin/codonw /usr/bin/transl
+/usr/bin/codonw /usr/bin/bases
+/usr/bin/codonw /usr/bin/base3s
+/usr/bin/codonw /usr/bin/dinuc
+/usr/bin/codonw /usr/bin/cai
+/usr/bin/codonw /usr/bin/fop
+/usr/bin/codonw /usr/bin/gc3s
+/usr/bin/codonw /usr/bin/gc
+/usr/bin/codonw /usr/bin/cbi
+/usr/bin/codonw /usr/bin/enc
\ No newline at end of file
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..13cdaf4
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/man/*.1
diff --git a/debian/patches/define_linux b/debian/patches/define_linux
new file mode 100644
index 0000000..5a07af3
--- /dev/null
+++ b/debian/patches/define_linux
@@ -0,0 +1,12 @@
+Description: Define_linux
+--- a/Makefile
++++ b/Makefile
+@@ -3,6 +3,8 @@
+
+ all: codonw
+
++CFLAGS+=-DLINUX
++
+ codonw: $(objects)
+ $(CC) $(CFLAGS) $(LDFLAGS) $(objects) -o codonw -lm
+
diff --git a/debian/patches/enable_clean b/debian/patches/enable_clean
new file mode 100644
index 0000000..7fa3a9b
--- /dev/null
+++ b/debian/patches/enable_clean
@@ -0,0 +1,30 @@
+Description: Enable_clean
+--- a/Makefile
++++ b/Makefile
+@@ -1,7 +1,7 @@
+ objects = codon_us.o codons.o open_fil.o commline.o menu.o tester.o coresp.o
+ linked = rscu cu aau raau tidy reader cutab cutot transl bases base3s dinuc cai fop gc3s gc cbi enc
+
+-all: codonw links
++all: codonw
+
+ codonw: $(objects)
+ $(CC) $(CFLAGS) $(LDFLAGS) $(objects) -o codonw -lm
+@@ -10,10 +10,10 @@
+ \rm -f $(objects)
+
+ cleanall:
+- \rm -f $(objects) codonw Makefile $(linked)
++ \rm -f $(objects) codonw $(linked)
+
+ realclean:
+- \rm -f $(objects) codonw Makefile $(linked)
++ \rm -f $(objects) codonw $(linked)
+
+ codon_us.o: codon_us.c codonW.h
+ $(CC) -c $(CFLAGS) $(CPPFLAGS) codon_us.c
+@@ -55,4 +55,3 @@
+ $(LN) codonw gc
+ $(LN) codonw cbi
+ $(LN) codonw enc
+-
diff --git a/debian/patches/hardening b/debian/patches/hardening
new file mode 100644
index 0000000..20a6396
--- /dev/null
+++ b/debian/patches/hardening
@@ -0,0 +1,62 @@
+Description: Hardening
+--- a/Makefile
++++ b/Makefile
+@@ -1,17 +1,10 @@
+-override cflags = $(CFLAGS) -g
+-
+ objects = codon_us.o codons.o open_fil.o commline.o menu.o tester.o coresp.o
+ linked = rscu cu aau raau tidy reader cutab cutot transl bases base3s dinuc cai fop gc3s gc cbi enc
+
+-CC=cc
+-CFLAGS= -O -DBSD
+-LN=ln -f
+-
+-
+-all: codonw links
++all: codonw links
+
+ codonw: $(objects)
+- $(CC) $(CFLAGS) $(objects) -o codonw -lm
++ $(CC) $(CFLAGS) $(LDFLAGS) $(objects) -o codonw -lm
+
+ clean:
+ \rm -f $(objects)
+@@ -22,26 +15,26 @@
+ realclean:
+ \rm -f $(objects) codonw Makefile $(linked)
+
+-codon_us.o: codon_us.c codonW.h
+- $(CC) -c $(CFLAGS) codon_us.c
++codon_us.o: codon_us.c codonW.h
++ $(CC) -c $(CFLAGS) $(CPPFLAGS) codon_us.c
+
+-menu.o: menu.c codonW.h
+- $(CC) -c $(CFLAGS) menu.c
++menu.o: menu.c codonW.h
++ $(CC) -c $(CFLAGS) $(CPPFLAGS) menu.c
+
+-codons.o: codons.c codonW.h
+- $(CC) -c $(CFLAGS) codons.c
++codons.o: codons.c codonW.h
++ $(CC) -c $(CFLAGS) $(CPPFLAGS) codons.c
+
+-coresp.o: coresp.c codonW.h
+- $(CC) -c $(CFLAGS) coresp.c
++coresp.o: coresp.c codonW.h
++ $(CC) -c $(CFLAGS) $(CPPFLAGS) coresp.c
+
+ open_fil.o: open_fil.c codonW.h
+- $(CC) -c $(CFLAGS) open_fil.c
++ $(CC) -c $(CFLAGS) $(CPPFLAGS) open_fil.c
+
+-commline.o: commline.c codonW.h
+- $(CC) -c $(CFLAGS) commline.c
++commline.o: commline.c codonW.h
++ $(CC) -c $(CFLAGS) $(CPPFLAGS) commline.c
+
+ tester.o: tester.c codonW.h
+- $(CC) -c $(CFLAGS) tester.c
++ $(CC) -c $(CFLAGS) $(CPPFLAGS) tester.c
+
+ links: codonw
+ $(LN) codonw rscu
diff --git a/debian/patches/hardening.patch b/debian/patches/hardening.patch
new file mode 100644
index 0000000..86a8411
--- /dev/null
+++ b/debian/patches/hardening.patch
@@ -0,0 +1,54 @@
+--- a/Makefile
++++ b/Makefile
+@@ -1,10 +1,17 @@
++override cflags = $(CFLAGS) -g
++
+ objects = codon_us.o codons.o open_fil.o commline.o menu.o tester.o coresp.o
+ linked = rscu cu aau raau tidy reader cutab cutot transl bases base3s dinuc cai fop gc3s gc cbi enc
+
++CC=cc
++CFLAGS= -O -DBSD
++LN=ln -f
++
++
+ all: codonw links
+
+ codonw: $(objects)
+- $(CC) $(CFLAGS) $(LDFLAGS) $(objects) -o codonw -lm
++ $(CC) $(CFLAGS) $(objects) -o codonw -lm
+
+ clean:
+ \rm -f $(objects)
+@@ -16,25 +23,25 @@
+ \rm -f $(objects) codonw Makefile $(linked)
+
+ codon_us.o: codon_us.c codonW.h
+- $(CC) -c $(CFLAGS) $(CPPFLAGS) codon_us.c
++ $(CC) -c $(CFLAGS) codon_us.c
+
+ menu.o: menu.c codonW.h
+- $(CC) -c $(CFLAGS) $(CPPFLAGS) menu.c
++ $(CC) -c $(CFLAGS) menu.c
+
+ codons.o: codons.c codonW.h
+- $(CC) -c $(CFLAGS) $(CPPFLAGS) codons.c
++ $(CC) -c $(CFLAGS) codons.c
+
+ coresp.o: coresp.c codonW.h
+- $(CC) -c $(CFLAGS) $(CPPFLAGS) coresp.c
++ $(CC) -c $(CFLAGS) coresp.c
+
+ open_fil.o: open_fil.c codonW.h
+- $(CC) -c $(CFLAGS) $(CPPFLAGS) open_fil.c
++ $(CC) -c $(CFLAGS) open_fil.c
+
+ commline.o: commline.c codonW.h
+- $(CC) -c $(CFLAGS) $(CPPFLAGS) commline.c
++ $(CC) -c $(CFLAGS) commline.c
+
+ tester.o: tester.c codonW.h
+- $(CC) -c $(CFLAGS) $(CPPFLAGS) tester.c
++ $(CC) -c $(CFLAGS) tester.c
+
+ links: codonw
+ $(LN) codonw rscu
diff --git a/debian/patches/remove_pause b/debian/patches/remove_pause
new file mode 100644
index 0000000..e5cfb32
--- /dev/null
+++ b/debian/patches/remove_pause
@@ -0,0 +1,27 @@
+Description: Remove_pause
+--- a/commline.c
++++ b/commline.c
+@@ -100,7 +100,6 @@
+ "positions\n"
+
+ );
+- pause;
+ printf(
+ " -L_sym\t\tNumber of synonymous codons\n"
+ " -L_aa\t\tTotal number of synonymous and non-synonymous codons\n"
+@@ -124,7 +123,6 @@
+ " -raau\t\tRelative Amino Acid Usage (RAAU)\n"
+ " -cu\t\tCodon Usage (CU) (default)\n"
+ );
+- pause;
+ printf(
+ " -cutab\t\tTabulation of codon usage\n"
+ " -cutot\t\tTabulation of dataset's codon usage\n"
+@@ -139,7 +137,6 @@
+ "\nWhere {file} represents an input filename, and N an integer"
+ " value"
+ );
+- pause;
+ my_exit(99,""); /* after writing out help quit */
+ }
+
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..950fc31
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,4 @@
+hardening
+enable_clean
+remove_pause
+define_linux
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..70638f0
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,26 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+
+%:
+ dh $@
+
+override_dh_clean:
+ rm -rf debian/man
+ dh_clean --exclude=Makefile.orig
+
+override_dh_auto_clean:
+ rm -rf *.o *.coa *.blk *.out *raw codonw codonW.log
+
+override_dh_auto_build:
+ $(MAKE) codonw
+
+override_dh_installman:
+ mkdir -p $(CURDIR)/debian/man
+ help2man -n 'Correspondence Analysis of Codon Usage' -N --help-option=-h --version-string=1.4.4 ./codonw > $(CURDIR)/debian/man/codonw.1
+ for i in rscu cu aau fop raau tidy reader cutab cutot transl bases base3s dinuc cai for gc3s gc cbi enc; do ln -s $(CURDIR)/debian/man/codonw.1 $(CURDIR)/debian/man/$$i.1; done
+ dh_installman --
+
+override_dh_auto_install:
+ mkdir -p debian/codonw/usr/bin
+ cp codonw debian/codonw/usr/bin
\ No newline at end of file
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/watch b/debian/watch
new file mode 100644
index 0000000..698d840
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=3
+opts="uversionmangle=s/_/./g" \
+http://sf.net/codonw/CodonWSourceCode_([0-9_]+)\.tar\.gz
--
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