[med-svn] r18644 - trunk/packages/barrnap/trunk/debian

[Sascha Steinbiss]

Author: sascha-guest
Date: 2015-01-30 21:17:07 +0000 (Fri, 30 Jan 2015)
New Revision: 18644

Added:
   trunk/packages/barrnap/trunk/debian/barrnap-silva-hmms.install
   trunk/packages/barrnap/trunk/debian/filter_hmms.lua
Modified:
   trunk/packages/barrnap/trunk/debian/barrnap.install
   trunk/packages/barrnap/trunk/debian/control
   trunk/packages/barrnap/trunk/debian/rules
Log:
split up HMMs to go into free and non-free packages


Added: trunk/packages/barrnap/trunk/debian/barrnap-silva-hmms.install
===================================================================
--- trunk/packages/barrnap/trunk/debian/barrnap-silva-hmms.install	                        (rev 0)
+++ trunk/packages/barrnap/trunk/debian/barrnap-silva-hmms.install	2015-01-30 21:17:07 UTC (rev 18644)
@@ -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

Modified: trunk/packages/barrnap/trunk/debian/barrnap.install
===================================================================
--- trunk/packages/barrnap/trunk/debian/barrnap.install	2015-01-30 18:46:23 UTC (rev 18643)
+++ trunk/packages/barrnap/trunk/debian/barrnap.install	2015-01-30 21:17:07 UTC (rev 18644)
@@ -1,2 +1,4 @@
 bin/barrnap usr/bin
-db usr/share/barrnap
+db/free/euk.hmm usr/share/barrnap/db
+db/free/arc.hmm usr/share/barrnap/db
+db/free/bac.hmm usr/share/barrnap/db

Modified: trunk/packages/barrnap/trunk/debian/control
===================================================================
--- trunk/packages/barrnap/trunk/debian/control	2015-01-30 18:46:23 UTC (rev 18643)
+++ trunk/packages/barrnap/trunk/debian/control	2015-01-30 21:17:07 UTC (rev 18644)
@@ -1,9 +1,8 @@
 Source: barrnap
-Section: non-free/science
 Priority: optional
 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), hmmer (>= 3.1)
+Build-Depends: debhelper (>= 9.0.0), hmmer (>= 3.1), lua5.1, dh-exec
 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/
@@ -11,6 +10,7 @@
 
 Package: barrnap
 Architecture: all
+Section: science
 Depends: ${perl:Depends}, ${shlibs:Depends}, ${misc:Depends}, hmmer (>= 3.1)
 Description: rapid ribosomal RNA prediction
  Barrnap (BAsic Rapid Ribosomal RNA Predictor) predicts the location of
@@ -21,3 +21,11 @@
  NHMMER tool that comes with HMMER 3.1 for HMM searching in RNA:DNA style.
  Multithreading is supported and one can expect roughly linear speed-ups
  with more CPUs.
+
+Package: barrnap-silva-hmms
+Architecture: any
+Section: non-free/science
+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.

Added: trunk/packages/barrnap/trunk/debian/filter_hmms.lua
===================================================================
--- trunk/packages/barrnap/trunk/debian/filter_hmms.lua	                        (rev 0)
+++ trunk/packages/barrnap/trunk/debian/filter_hmms.lua	2015-01-30 21:17:07 UTC (rev 18644)
@@ -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/trunk/debian/filter_hmms.lua
___________________________________________________________________
Added: svn:executable
   + *

Modified: trunk/packages/barrnap/trunk/debian/rules
===================================================================
--- trunk/packages/barrnap/trunk/debian/rules	2015-01-30 18:46:23 UTC (rev 18643)
+++ trunk/packages/barrnap/trunk/debian/rules	2015-01-30 21:17:07 UTC (rev 18644)
@@ -10,12 +10,22 @@
 	dh $@ --parallel
 
 override_dh_auto_build:
-	# pass
+	mkdir db/free
+	debian/filter_hmms.lua 28S   < db/euk.hmm > db/free/euk.hmm
+	debian/filter_hmms.lua 23S   < db/arc.hmm > db/free/arc.hmm
+	debian/filter_hmms.lua 23S   < db/bac.hmm > db/free/bac.hmm
+	mkdir db/nonfree
+	debian/filter_hmms.lua 28S t < db/euk.hmm > db/nonfree/euk.hmm
+	debian/filter_hmms.lua 23S t < db/arc.hmm > db/nonfree/arc.hmm
+	debian/filter_hmms.lua 23S t < db/bac.hmm > db/nonfree/bac.hmm
 
 override_dh_auto_install:
-	# pass 
+	# pass
 
+override_dh_auto_clean:
+	rm -rf db/free db/nonfree
+
 get-orig-source:
 	uscan --verbose --force-download --repack --compression xz --destdir=..
-	mv ../barrnap_$(OVERSION).orig.tar.xz ../barrnap_$(VERSION).orig.tar.xz 
+	mv ../barrnap_$(OVERSION).orig.tar.xz ../barrnap_$(VERSION).orig.tar.xz