[med-svn] [suitename] 02/02: Add initial packaging
Andreas Tille
tille at debian.org
Wed Jul 22 08:34:19 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository suitename.
commit fab61095f2f027d99dffd19ea431ea20fd945d2d
Author: Andreas Tille <tille at debian.org>
Date: Wed Jul 22 10:33:57 2015 +0200
Add initial packaging
---
debian/changelog | 5 +++
debian/clean | 1 +
debian/compat | 1 +
debian/control | 26 +++++++++++++
debian/copyright | 19 +++++++++
debian/install | 1 +
debian/manpages | 1 +
debian/patches/hardening.patch | 15 ++++++++
debian/patches/series | 1 +
debian/rules | 23 +++++++++++
debian/source/format | 1 +
debian/suitename.1 | 87 ++++++++++++++++++++++++++++++++++++++++++
debian/upstream/metadata | 12 ++++++
debian/watch | 6 +++
14 files changed, 199 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..23ace7a
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+suitename (0.3.070628-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org> Wed, 22 Jul 2015 09:44:21 +0200
diff --git a/debian/clean b/debian/clean
new file mode 100644
index 0000000..50bc60b
--- /dev/null
+++ b/debian/clean
@@ -0,0 +1 @@
+suitename
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..7bb28d9
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,26 @@
+Source: suitename
+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: 3.9.6
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/suitename.git
+Vcs-Git: git://anonscm.debian.org/debian-med/suitename.git
+Homepage: http://kinemage.biochem.duke.edu/software/suitename.php
+
+Package: suitename
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: categorize each suite in an RNA backbone
+ Suitename is a program that supports the ROC RNA Ontology Consortium
+ consensus RNA backbone nomenclature and conformer-list development.
+ .
+ From dihedral-angle input for a specific RNA structure (usually from
+ Dangle), Suitename categorizes the RNA backbone geometry of each suite
+ (the sugar-to-sugar version of a residue) either as an outlier ("!!") or
+ as belonging to one of the 53 defined conformer bins. The output is
+ either a one-line-per-suite report, or a linear conformer string (as
+ shown below the image here) in one of several variant formats. Suitename
+ is built into MolProbity, producing entries in the multi-criterion chart
+ for an RNA model and also a suitestring file.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..88ff73d
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,19 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: suitename
+Source: https://github.com/rlabduke/suitename/
+
+Files: *
+Copyright: 2007 David C. Richardson
+License: suitename
+
+Files: debian/*
+Copyright: 2015 Andreas Tille <tille at debian.org>
+License: suitename
+
+License: suitename
+ This is free software and the source code is freely
+ available. You are free to redistribute or modify under the
+ conditions that (1) this notice is not removed or modified
+ in any way and (2) any modified versions of the program are
+ also available for free.
+ ** Absolutely no Warranty **
diff --git a/debian/install b/debian/install
new file mode 100644
index 0000000..f7448db
--- /dev/null
+++ b/debian/install
@@ -0,0 +1 @@
+suitename usr/bin
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..0f65186
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/*.1
diff --git a/debian/patches/hardening.patch b/debian/patches/hardening.patch
new file mode 100644
index 0000000..472a5d2
--- /dev/null
+++ b/debian/patches/hardening.patch
@@ -0,0 +1,15 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Wed, 22 Jul 2015 09:44:21 +0200
+Description: Propagate hardening options
+
+--- a/Makefile.linux
++++ b/Makefile.linux
+@@ -15,7 +15,7 @@ OBJS = suitename.o suitenscrt.o suitenin
+ # ---------------------------------------------------------------------
+ HEADERS = suitename.h suitenscrt.h suitenutil.h suiteninit.h suiteninpt.h suitenout.h
+ suitename: $(OBJS)
+- cc -o suitename $(CFLAGS) $(OBJS) $(LIBS)
++ cc -o suitename $(CFLAGS) $(OBJS) $(LIBS) $(LDFLAGS)
+
+ debug: $(OBJS)
+ cc -o suitename $(CFLAGS) $(OBJS) $(LIBS)
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..814900f
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+hardening.patch
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..e010d7f
--- /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 $@
+
+override_dh_auto_build:
+ dh_auto_build --buildsystem=makefile -- -f Makefile.linux suitename
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/suitename.1 b/debian/suitename.1
new file mode 100644
index 0000000..7dcfcd2
--- /dev/null
+++ b/debian/suitename.1
@@ -0,0 +1,87 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.1.
+.TH SUITENAME "1" "July 2015" "suitename 0.3.070628" "User Commands"
+.SH NAME
+suitename \- categorize each suite in an RNA backbone as belonging to either one of 53 defined types or as outlier
+.SH SYNOPSIS
+.B suitename
+\fB\-flags\fR <stdin >stdout
+.SH DESCRIPTION
+.P
+Suitename is a program that supports the ROC RNA Ontology Consortium
+consensus RNA backbone nomenclature and conformer-list development.
+.P
+From dihedral-angle input for a specific RNA structure (usually from
+Dangle), Suitename categorizes the RNA backbone geometry of each suite
+(the sugar-to-sugar version of a residue) either as an outlier ("!!") or
+as belonging to one of the 53 defined conformer bins. The output is
+either a one-line-per-suite report, or a linear conformer string (as
+shown below the image here) in one of several variant formats. Suitename
+is built into MolProbity, producing entries in the multi-criterion chart
+for an RNA model and also a suitestring file.
+.SH OPTIONS
+.IP
+output flags: [ \fB\-report\fR || \fB\-string\fR || \fB\-kinemage\fR ]
+.IP
+default: \fB\-report\fR \fB\-residuein\fR
+.IP
+input flags: [ \fB\-residuein\fR || \fB\-suitein\fR ]
+.IP
+flags: [ \fB\-residuein\fR [ \fB\-pointIDfields\fR # ] ] default#==6
+.IP
+OR flags: [ \fB\-suitein\fR [ \fB\-anglefields\fR # ] ] default#==9
+.IP
+defaults: \fB\-residuein\fR \fB\-pointIDfields\fR 6
+as made by dangle
+.IP
+dangle "alpha, beta, gamma, delta, epsilon, zeta" in.pdb >out.dngl
+.IP
+label:model:chain:number:ins:type:alpha:beta:gamma:delta:epsilon:zeta
+.IP
+\fB\-suitein\fR presumes point records from a kinemage
+{pointID} 7 or 9 anglefields
+{ptID} [chi] deltam epsilon zeta alpha beta gamma delta [chi]
+.PP
+Note that all other kinemage lines must be stripped off.
+.IP
+\fB\-thetaeta\fR kinemage labels theta,eta instead of chi\-1,chi
+.PP
+Note dangle trick to make theta,...,eta suites directly
+.IP
+flag: \fB\-report\fR [ \fB\-chart\fR ]
+suites in order of input, suiteness summary at end
+.IP
+( \fB\-chart\fR : NO summary at end, for MolProbity multichart)
+.IP
+flag: \fB\-string\fR
+3 character per suite string in order of input
+.IP
+20 per line, ptID of n*20th at end of line
+.IP
+flag: \fB\-nosequence\fR
+only suite names, no Base sequence character
+.IP
+flag: \fB\-oneline\fR
+string all one line, no point IDs
+.IP
+flag: \fB\-overlap\fR
+20 per line: overlap 10 each line, 10 new per line
+.IP
+flag: \fB\-kinemage\fR
+kinemage of clusters grouped by pucker,pucker ...
+.IP
+group {delta,delta},subgroup {gamma},list {cluster name}
+assigns to designated wannabe clusters, default: wannabe
+.IP
+flag: \fB\-nowannabe\fR to not assign them
+.IP
+[ \fB\-power\fR #.#] default# 3.00 multi\-dimension distance calc
+.IP
+[ \fB\-test\fR ] dump cluster centers, halfwidths,... to stderr
+.PP
+cluster averages version: 070506
+.PP
+cluster half\-widths version: 070328
+.PP
+axes limits version: 070326
+.PP
+suitename is not paying attention to chains...
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..22997d0
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,12 @@
+Reference:
+ Author: Jane S. Richardson and Bohdan Schneider and Laura W. Murray and Gary J. Kapral and Robert M. Immormino and Jeffrey J. Headd and David C. Richardson and Daniela Ham and Eli Hershkovits and Loren Dean Williams and Kevin S. Keating and Anna Marie Pyle and David Micallef and John Westbrook and Helen M. Berman
+ Title: "RNA backbone: Consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution)"
+ Journal: RNA
+ Year: 2008
+ Volume: 14
+ Number: 3
+ Pages: 465-481
+ DOI: 10.1261/rna.657708
+ PMID: 18192612
+ URL: http://rnajournal.cshlp.org/content/14/3/465
+ eprint: http://rnajournal.cshlp.org/content/14/3/465.full.pdf+html
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..2877407
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,6 @@
+version=3
+
+http://kinemage.biochem.duke.edu/software/suitename.php .*/downloads/software/suitename/suitename.([\d.]+)\.src\.tgz
+
+# if there would be release tags ...
+# https://github.com/rlabduke/suitename/releases .*/archive/#PREFIX#(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
--
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