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 <[email protected]> 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 <[email protected]> +Uploaders: Andreas Tille <[email protected]> +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 <[email protected]> +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 <[email protected]> +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))) _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
