[med-svn] r18672 - in trunk/packages: . barrnap/trunk/debian barrnap-data-nonfree barrnap-data-nonfree/trunk barrnap-data-nonfree/trunk/debian barrnap-data-nonfree/trunk/debian/source
Sascha Steinbiss
sascha-guest at moszumanska.debian.org
Sat Jan 31 14:31:21 UTC 2015
Author: sascha-guest
Date: 2015-01-31 14:31:20 +0000 (Sat, 31 Jan 2015)
New Revision: 18672
Added:
trunk/packages/barrnap-data-nonfree/
trunk/packages/barrnap-data-nonfree/trunk/
trunk/packages/barrnap-data-nonfree/trunk/debian/
trunk/packages/barrnap-data-nonfree/trunk/debian/barrnap-silva-hmms.install
trunk/packages/barrnap-data-nonfree/trunk/debian/changelog
trunk/packages/barrnap-data-nonfree/trunk/debian/compat
trunk/packages/barrnap-data-nonfree/trunk/debian/control
trunk/packages/barrnap-data-nonfree/trunk/debian/copyright
trunk/packages/barrnap-data-nonfree/trunk/debian/files
trunk/packages/barrnap-data-nonfree/trunk/debian/filter_hmms.lua
trunk/packages/barrnap-data-nonfree/trunk/debian/rules
trunk/packages/barrnap-data-nonfree/trunk/debian/source/
trunk/packages/barrnap-data-nonfree/trunk/debian/source/format
trunk/packages/barrnap-data-nonfree/trunk/debian/watch
Modified:
trunk/packages/barrnap/trunk/debian/control
Log:
rename barrnap data package
Modified: trunk/packages/barrnap/trunk/debian/control
===================================================================
--- trunk/packages/barrnap/trunk/debian/control 2015-01-31 14:22:53 UTC (rev 18671)
+++ trunk/packages/barrnap/trunk/debian/control 2015-01-31 14:31:20 UTC (rev 18672)
@@ -12,7 +12,7 @@
Package: barrnap
Architecture: all
Depends: ${perl:Depends}, ${shlibs:Depends}, ${misc:Depends}, hmmer (>= 3.1)
-Suggests: barrnap-silva-hmms
+Suggests: barrnap-data-nonfree
Description: rapid ribosomal RNA prediction
Barrnap (BAsic Rapid Ribosomal RNA Predictor) predicts the location of
ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea
Added: trunk/packages/barrnap-data-nonfree/trunk/debian/barrnap-silva-hmms.install
===================================================================
--- trunk/packages/barrnap-data-nonfree/trunk/debian/barrnap-silva-hmms.install (rev 0)
+++ trunk/packages/barrnap-data-nonfree/trunk/debian/barrnap-silva-hmms.install 2015-01-31 14:31:20 UTC (rev 18672)
@@ -0,0 +1,3 @@
+db/nonfree/euk.hmm usr/share/barrnap/db/nonfree
+db/nonfree/arc.hmm usr/share/barrnap/db/nonfree
+db/nonfree/bac.hmm usr/share/barrnap/db/nonfree
Added: trunk/packages/barrnap-data-nonfree/trunk/debian/changelog
===================================================================
--- trunk/packages/barrnap-data-nonfree/trunk/debian/changelog (rev 0)
+++ trunk/packages/barrnap-data-nonfree/trunk/debian/changelog 2015-01-31 14:31:20 UTC (rev 18672)
@@ -0,0 +1,5 @@
+barrnap-data-nonfree (0.5-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #XXX)
+
+ -- Sascha Steinbiss <sascha at steinbiss.name> Sat, 31 Jan 2015 10:12:42 +0000
Added: trunk/packages/barrnap-data-nonfree/trunk/debian/compat
===================================================================
--- trunk/packages/barrnap-data-nonfree/trunk/debian/compat (rev 0)
+++ trunk/packages/barrnap-data-nonfree/trunk/debian/compat 2015-01-31 14:31:20 UTC (rev 18672)
@@ -0,0 +1 @@
+9
Added: trunk/packages/barrnap-data-nonfree/trunk/debian/control
===================================================================
--- trunk/packages/barrnap-data-nonfree/trunk/debian/control (rev 0)
+++ trunk/packages/barrnap-data-nonfree/trunk/debian/control 2015-01-31 14:31:20 UTC (rev 18672)
@@ -0,0 +1,18 @@
+Source: barrnap-data-nonfree
+Priority: extra
+Section: non-free/science
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Sascha Steinbiss <sascha at steinbiss.name>
+Build-Depends: debhelper (>= 9.0.0), lua5.1
+Standards-Version: 3.9.6
+Homepage: http://www.vicbioinformatics.com/software.barrnap.shtml
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/barrnap/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/barrnap/trunk/
+
+Package: barrnap-data-nonfree
+Architecture: any
+Depends: ${misc:Depends}, barrnap
+Description: non-free pHMMs for barrnap
+ Profile Hidden Markov models (pHMMs) for use with Barrnap (BAsic Rapid
+ Ribosomal RNA Predictor), which are only free to use for academic users.
+ In particular, these are the 28S (euk) and 23S (arc, bac) rRNAs.
Added: trunk/packages/barrnap-data-nonfree/trunk/debian/copyright
===================================================================
--- trunk/packages/barrnap-data-nonfree/trunk/debian/copyright (rev 0)
+++ trunk/packages/barrnap-data-nonfree/trunk/debian/copyright 2015-01-31 14:31:20 UTC (rev 18672)
@@ -0,0 +1,50 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: barrnap
+Source: https://github.com/Victorian-Bioinformatics-Consortium/barrnap
+
+Files: debian/*
+Copyright:
+ Copyright 2015 Sascha Steinbiss <sascha at steinbiss.name>
+License: ISC
+ Permission to use, copy, modify, and/or distribute this software for any
+ purpose with or without fee is hereby granted, provided that the above
+ copyright notice and this permission notice appear in all copies.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH
+ REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND
+ FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT,
+ INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM
+ LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR
+ OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR
+ PERFORMANCE OF THIS SOFTWARE.
+
+Files: db/*
+Copyright:
+ Copyright 2007-2013 The SILVA ribosomal RNA database project <contact at arb-silva.de>
+License: SILVA_non_free
+ The HMMs in the db/ directory have been built from data sources including one
+ covered by the following license:
+ .
+ The SILVA database content offered at www.arb-silva.de can be freely browsed
+ and the corresponding information deployed by all users, independent from
+ their status (academic or non-academic).
+ .
+ All downloads are free for academic users. They can be used, modified and
+ redistributed within the academic environment without any limitation.
+ However, in case of redistribution please make transparent the SILVA Terms
+ of Use/License Information by linking/referring to this page (see link in
+ the header of your browser). Academic users are represented by universities
+ and non-commercial research institutes such as members of the German
+ Helmholtz Association, Leibniz Association and Max-Planck Society as well as
+ US National Labs.
+ .
+ Users from NON-ACADEMIC can also directly access all downloads including the
+ results of the SILVA web-aligner (SINA) but only for limited/temporary use
+ (only for test purposes). All downloaded files should be deleted latest
+ after 48 hours. Unauthorized usage beyond test purposes is strictly
+ prohibited. If you are interested in unlimited usage of the SILVA
+ databases/services (e.g. the web-aligner) or parts of them within a
+ non-academic environment, please contact us for more information at
+ contact(at)arb-silva.de. A non-academic environment is defined by a direct
+ or indirect commercial interest in the data and includes all industrial
+ research entities.
Added: trunk/packages/barrnap-data-nonfree/trunk/debian/files
===================================================================
--- trunk/packages/barrnap-data-nonfree/trunk/debian/files (rev 0)
+++ trunk/packages/barrnap-data-nonfree/trunk/debian/files 2015-01-31 14:31:20 UTC (rev 18672)
@@ -0,0 +1 @@
+barrnap_0.5-1_all.deb science optional
Added: trunk/packages/barrnap-data-nonfree/trunk/debian/filter_hmms.lua
===================================================================
--- trunk/packages/barrnap-data-nonfree/trunk/debian/filter_hmms.lua (rev 0)
+++ trunk/packages/barrnap-data-nonfree/trunk/debian/filter_hmms.lua 2015-01-31 14:31:20 UTC (rev 18672)
@@ -0,0 +1,35 @@
+#!/usr/bin/env lua
+
+function usage()
+ io.stderr:write(string.format("Usage: %s <filter> [<invert>] < file\n", arg[0]))
+ io.stderr:write('Filters out a HMM with NAME matching <filter>.\n')
+ os.exit(1)
+end
+
+if #arg < 1 then
+ usage()
+end
+
+lastname = nil
+lines = {}
+for l in io.lines() do
+ name = l:match('NAME%s+(.*)')
+ table.insert(lines, l)
+ if name then
+ lastname = name
+ elseif l:match('//') then
+ if arg[2] then
+ if lastname:match(arg[1]) then
+ print(table.concat(lines, '\n'))
+ end
+ else
+ if not lastname:match(arg[1]) then
+ print(table.concat(lines, '\n'))
+ end
+ end
+ lines = {}
+ end
+end
+
+
+
Property changes on: trunk/packages/barrnap-data-nonfree/trunk/debian/filter_hmms.lua
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/barrnap-data-nonfree/trunk/debian/rules
===================================================================
--- trunk/packages/barrnap-data-nonfree/trunk/debian/rules (rev 0)
+++ trunk/packages/barrnap-data-nonfree/trunk/debian/rules 2015-01-31 14:31:20 UTC (rev 18672)
@@ -0,0 +1,40 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+
+DH_VERBOSE=1
+DEBVERS := $(shell dpkg-parsechangelog | sed -n -e 's/^Version: //p')
+VERSION := $(shell echo '$(DEBVERS)' | sed -e 's/^[[:digit:]]*://' -e 's/[~-].*//')
+OVERSION := $(shell echo '$(DEBVERS)' | sed -e 's/^[[:digit:]]*://' -e 's/[+].*//')
+
+%:
+ dh $@ --parallel
+
+override_dh_auto_build:
+ # pass
+
+override_dh_auto_install:
+ # pass
+
+override_dh_auto_clean:
+ rm -rf db/free
+
+get-orig-source:
+ uscan --verbose --force-download --repack --compression xz --destdir=..
+ unxz ../barrnap-data-nonfree_$(OVERSION).orig.tar.xz
+ mkdir -p debian/repack-tmp
+ tar xf ../barrnap-data-nonfree_$(OVERSION).orig.tar -C debian/repack-tmp
+ rm ../barrnap-data-nonfree_$(OVERSION).orig.tar
+ mkdir -p debian/repack-tmp/barrnap-data-nonfree_$(OVERSION)/db/nonfree
+ debian/filter_hmms.lua 28S t < \
+ debian/repack-tmp/barrnap-$(OVERSION)/db/euk.hmm > \
+ debian/repack-tmp/barrnap-data-nonfree_$(OVERSION)/db/nonfree/euk.hmm
+ debian/filter_hmms.lua 23S t < \
+ debian/repack-tmp/barrnap-$(OVERSION)/db/arc.hmm > \
+ debian/repack-tmp/barrnap-data-nonfree_$(OVERSION)/db/nonfree/arc.hmm
+ debian/filter_hmms.lua 23S t < \
+ debian/repack-tmp/barrnap-$(OVERSION)/db/bac.hmm > \
+ debian/repack-tmp/barrnap-data-nonfree_$(OVERSION)/db/nonfree/bac.hmm
+ rm -rf debian/repack-tmp/barrnap-$(OVERSION)
+ tar cf ../barrnap-data-nonfree_$(VERSION).orig.tar -C debian/repack-tmp barrnap-data-nonfree_$(OVERSION)
+ xz ../barrnap-data-nonfree_$(VERSION).orig.tar
+ rm -rf debian/repack-tmp
Property changes on: trunk/packages/barrnap-data-nonfree/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/barrnap-data-nonfree/trunk/debian/source/format
===================================================================
--- trunk/packages/barrnap-data-nonfree/trunk/debian/source/format (rev 0)
+++ trunk/packages/barrnap-data-nonfree/trunk/debian/source/format 2015-01-31 14:31:20 UTC (rev 18672)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/barrnap-data-nonfree/trunk/debian/watch
===================================================================
--- trunk/packages/barrnap-data-nonfree/trunk/debian/watch (rev 0)
+++ trunk/packages/barrnap-data-nonfree/trunk/debian/watch 2015-01-31 14:31:20 UTC (rev 18672)
@@ -0,0 +1,4 @@
+version=3
+
+opts=filenamemangle=s/.+\/v?(\d\S*)\.tar\.gz/barrnap-$1.tar.gz/,dversionmangle=s/.dfsg// \
+ https://github.com/Victorian-Bioinformatics-Consortium/barrnap/tags .*/v?(\d\S*)\.tar\.gz
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