[med-svn] r16600 - in trunk/packages: . smalt smalt/trunk smalt/trunk/debian smalt/trunk/debian/mans smalt/trunk/debian/source
Andreas Tille
tille at moszumanska.debian.org
Tue Apr 8 13:44:04 UTC 2014
Author: tille
Date: 2014-04-08 13:44:03 +0000 (Tue, 08 Apr 2014)
New Revision: 16600
Added:
trunk/packages/smalt/
trunk/packages/smalt/trunk/
trunk/packages/smalt/trunk/debian/
trunk/packages/smalt/trunk/debian/changelog
trunk/packages/smalt/trunk/debian/compat
trunk/packages/smalt/trunk/debian/control
trunk/packages/smalt/trunk/debian/copyright
trunk/packages/smalt/trunk/debian/createmanpages
trunk/packages/smalt/trunk/debian/manpages
trunk/packages/smalt/trunk/debian/mans/
trunk/packages/smalt/trunk/debian/mans/smalt.1
trunk/packages/smalt/trunk/debian/rules
trunk/packages/smalt/trunk/debian/source/
trunk/packages/smalt/trunk/debian/source/format
trunk/packages/smalt/trunk/debian/watch
Log:
Inject initial packaging for SMALT (not finished yet)
Added: trunk/packages/smalt/trunk/debian/changelog
===================================================================
--- trunk/packages/smalt/trunk/debian/changelog (rev 0)
+++ trunk/packages/smalt/trunk/debian/changelog 2014-04-08 13:44:03 UTC (rev 16600)
@@ -0,0 +1,5 @@
+smalt (0.7.6-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org> Tue, 08 Apr 2014 10:12:51 +0200
Added: trunk/packages/smalt/trunk/debian/compat
===================================================================
--- trunk/packages/smalt/trunk/debian/compat (rev 0)
+++ trunk/packages/smalt/trunk/debian/compat 2014-04-08 13:44:03 UTC (rev 16600)
@@ -0,0 +1 @@
+9
Added: trunk/packages/smalt/trunk/debian/control
===================================================================
--- trunk/packages/smalt/trunk/debian/control (rev 0)
+++ trunk/packages/smalt/trunk/debian/control 2014-04-08 13:44:03 UTC (rev 16600)
@@ -0,0 +1,20 @@
+Source: smalt
+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/smalt/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/smalt/trunk/
+Homepage: http://www.sanger.ac.uk/resources/software/smalt/
+
+Package: smalt
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: efficiently align DNA sequencing reads with a reference genome
+ SMALT efficiently aligns DNA sequencing reads with a reference genome.
+ Reads from a wide range of sequencing platforms, for example Illumina,
+ Roche-454, Ion Torrent, PacBio or ABI-Sanger, can be processed including
+ paired reads.
+
Added: trunk/packages/smalt/trunk/debian/copyright
===================================================================
--- trunk/packages/smalt/trunk/debian/copyright (rev 0)
+++ trunk/packages/smalt/trunk/debian/copyright 2014-04-08 13:44:03 UTC (rev 16600)
@@ -0,0 +1,30 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: SMALT
+Upstream-Contact: Hannes Ponstingl <hp3 at sanger.ac.uk>
+Source: http://sourceforge.net/projects/smalt/files/
+
+Files: *
+Copyright: 2010-2014 Hannes Ponstingl at the Wellcome Trust Sanger Institute, Cambridge, UK
+License: GPL-3
+
+Files: debian/*
+Copyright: 2014 Andreas Tille <tille at debian.org>
+License: GPL-3
+
+License: GPL-3
+ 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 3 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, see <http://www.gnu.org/licenses/>.
+ .
+ On Debian Systems you can find a copy of the text of GPL version 3
+ at /usr/share/common-licenses/GPL-3.
+
Added: trunk/packages/smalt/trunk/debian/createmanpages
===================================================================
--- trunk/packages/smalt/trunk/debian/createmanpages (rev 0)
+++ trunk/packages/smalt/trunk/debian/createmanpages 2014-04-08 13:44:03 UTC (rev 16600)
@@ -0,0 +1,12 @@
+#!/bin/sh
+MANDIR=debian/mans
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//'`
+
+help2man --no-info --no-discard-stderr --help-option=" " \
+ --name='<optional description of the program>' \
+ --version-string="$VERSION" smalt > $MANDIR/smalt.1
+#help2man --no-info --no-discard-stderr --help-option=" " \
+# --name='<optional description of the program>' \
+# --version-string="$VERSION" basqcol > $MANDIR/basqcol.1
Property changes on: trunk/packages/smalt/trunk/debian/createmanpages
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/smalt/trunk/debian/manpages
===================================================================
--- trunk/packages/smalt/trunk/debian/manpages (rev 0)
+++ trunk/packages/smalt/trunk/debian/manpages 2014-04-08 13:44:03 UTC (rev 16600)
@@ -0,0 +1 @@
+debian/mans/*.1
Added: trunk/packages/smalt/trunk/debian/mans/smalt.1
===================================================================
--- trunk/packages/smalt/trunk/debian/mans/smalt.1 (rev 0)
+++ trunk/packages/smalt/trunk/debian/mans/smalt.1 2014-04-08 13:44:03 UTC (rev 16600)
@@ -0,0 +1,32 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.45.1.
+.TH SMALT "1" "April 2014" "smalt 0.7.6" "User Commands"
+.SH NAME
+smalt \- <optional description of the program>
+.SH DESCRIPTION
+.TP
+SMALT \- Sequence Mapping and Alignment Tool
+(version: 0.7.6)
+.SS "SYNOPSIS:"
+.IP
+smalt <task> [TASK_OPTIONS] [<index_name> <file_name_A> [<file_name_B>]]
+.SS "Available tasks:"
+.TP
+smalt check
+\- checks FASTA/FASTQ input
+.TP
+smalt help
+\- prints a brief summary of this software
+.TP
+smalt index
+\- builds an index of k\-mer words for the reference
+.TP
+smalt map
+\- maps single or paired reads onto the reference
+.TP
+smalt sample
+\- sample insert sizes for paired reads
+.IP
+smalt version \- prints version information
+.SS "Help on individual tasks:"
+.IP
+smalt <task> \fB\-H\fR
Added: trunk/packages/smalt/trunk/debian/rules
===================================================================
--- trunk/packages/smalt/trunk/debian/rules (rev 0)
+++ trunk/packages/smalt/trunk/debian/rules 2014-04-08 13:44:03 UTC (rev 16600)
@@ -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
Property changes on: trunk/packages/smalt/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/smalt/trunk/debian/source/format
===================================================================
--- trunk/packages/smalt/trunk/debian/source/format (rev 0)
+++ trunk/packages/smalt/trunk/debian/source/format 2014-04-08 13:44:03 UTC (rev 16600)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/smalt/trunk/debian/watch
===================================================================
--- trunk/packages/smalt/trunk/debian/watch (rev 0)
+++ trunk/packages/smalt/trunk/debian/watch 2014-04-08 13:44:03 UTC (rev 16600)
@@ -0,0 +1,2 @@
+version=3
+http://sf.net/smalt/smalt-(\d[\d\.]+)\.(?:tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz)))
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