[med-svn] [barrnap-data-nonfree] 01/13: rename barrnap data package
Andreas Tille
tille at debian.org
Fri Dec 29 21:31:37 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository barrnap-data-nonfree.
commit 3fcae888e0a41790525fa52cea0294466aa0302d
Author: Sascha Steinbiss <satta at debian.org>
Date: Sat Jan 31 14:31:20 2015 +0000
rename barrnap data package
---
debian/barrnap-silva-hmms.install | 3 +++
debian/changelog | 5 ++++
debian/compat | 1 +
debian/control | 18 ++++++++++++++
debian/copyright | 50 +++++++++++++++++++++++++++++++++++++++
debian/files | 1 +
debian/filter_hmms.lua | 35 +++++++++++++++++++++++++++
debian/rules | 40 +++++++++++++++++++++++++++++++
debian/source/format | 1 +
debian/watch | 4 ++++
10 files changed, 158 insertions(+)
diff --git a/debian/barrnap-silva-hmms.install b/debian/barrnap-silva-hmms.install
new file mode 100644
index 0000000..6ff5727
--- /dev/null
+++ b/debian/barrnap-silva-hmms.install
@@ -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
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..a5ceca2
--- /dev/null
+++ b/debian/changelog
@@ -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
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..84d4902
--- /dev/null
+++ b/debian/control
@@ -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.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..5b2eb6a
--- /dev/null
+++ b/debian/copyright
@@ -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.
diff --git a/debian/files b/debian/files
new file mode 100644
index 0000000..8f5dd7d
--- /dev/null
+++ b/debian/files
@@ -0,0 +1 @@
+barrnap_0.5-1_all.deb science optional
diff --git a/debian/filter_hmms.lua b/debian/filter_hmms.lua
new file mode 100755
index 0000000..f000948
--- /dev/null
+++ b/debian/filter_hmms.lua
@@ -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
+
+
+
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..135b261
--- /dev/null
+++ b/debian/rules
@@ -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
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..16515b4
--- /dev/null
+++ b/debian/watch
@@ -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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