[med-svn] r16651 - in trunk/packages/acacia/trunk/debian: . bin source
Timothy Booth
tbooth-guest at moszumanska.debian.org
Thu Apr 10 13:18:12 UTC 2014
Author: tbooth-guest
Date: 2014-04-10 13:18:12 +0000 (Thu, 10 Apr 2014)
New Revision: 16651
Added:
trunk/packages/acacia/trunk/debian/README.source
trunk/packages/acacia/trunk/debian/acacia.desktop
trunk/packages/acacia/trunk/debian/acacia.docs
trunk/packages/acacia/trunk/debian/acacia.install
trunk/packages/acacia/trunk/debian/acacia.jlibs
trunk/packages/acacia/trunk/debian/bin/
trunk/packages/acacia/trunk/debian/bin/acacia
trunk/packages/acacia/trunk/debian/changelog
trunk/packages/acacia/trunk/debian/classpath.sh
trunk/packages/acacia/trunk/debian/compat
trunk/packages/acacia/trunk/debian/control
trunk/packages/acacia/trunk/debian/copyright
trunk/packages/acacia/trunk/debian/rules
trunk/packages/acacia/trunk/debian/source/
trunk/packages/acacia/trunk/debian/source/format
trunk/packages/acacia/trunk/debian/watch
Log:
Working acacia package.
If we can just get an answer regarding Colt this should be DFSG.
Added: trunk/packages/acacia/trunk/debian/README.source
===================================================================
--- trunk/packages/acacia/trunk/debian/README.source (rev 0)
+++ trunk/packages/acacia/trunk/debian/README.source 2014-04-10 13:18:12 UTC (rev 16651)
@@ -0,0 +1,55 @@
+Where did I get to with packaging Acacia??
+
+I was working my way through the deps, and I had some files scattered somewhere. Where are they??
+Ah yes - hidden as a draft e-mail, of course! Here you go:
+
+
+org/eclipse/jdt/internal/jarinjarloader - not needed as we'll not
+package like that
+
+ # biojava.jar (?version unknown?)
+ # biojava-1.7.1-all.jar = libbiojava1.7
+ # classmexer-0_03.zip (a red herring? maybe only needed for testing)
+ # colt.jar =
+http://acs.lbl.gov/software/colt/colt-download/releases/colt-1.2.0.tar.gz
+ # optimization.jar = http://www1.fpl.fs.fed.us/optimization.html (or
+the newer version??)
+ # Blas.jar = http://www1.fpl.fs.fed.us/Blas_f77.html, but already in optimization.jar
+ # tcode.jar = see ssj
+ # jfreechart-1.0.10.jar - already in Debian
+ # jcommon-1.0.13.jar - ditto
+ # language-1.6.7.jar - in dsol
+ # event-1.6.5.jar - in dsol
+ # logger-1.6.4.jar - in dsol
+ # interpreter-1.6.8.jar - in dsol
+ # ssj.jar = http://www.iro.umontreal.ca/~simardr/ssj/ssj-source.html
+ # needs Tcode and various jars, plus:
+ http://statistik.wu-wien.ac.at/unuran/download.html
+ which wants:
+ http://statistik.wu-wien.ac.at/software/RngStreams/
+ # commons-cli-1.2.jar = libcommons-cli-java
+ # commons-math-2.1.jar = libcommons-math-java
+
+Also, SSJ might or might not need libdsol1-xml-java which in turn is a
+PITA. See readme.tim in libdsol1-xml-java.
+
+SSJ definitely does need colt, so let's package colt before going any further.
+Ah - Andreas already started:
+http://svn.debian.org/wsvn/debian-med/trunk/packages/libcolt-java/trunk/
+
+Need to talk to the Java guys and see who is packaging what, and to look
+for any ITP entries.
+
+---
+
+Hmmm - the Debian folder here still has files unmodified from King. Oh yes, I was stuck on libdsol1-xml-java. Back to that.
+
+It looks like there is a newer Acacia binary but no source. No matter, I shall press on with 1.52.
+
+...
+
+Right, by the looks of it I can build ssj.jar without unuran jni support, which makes life simpler. I may as
+well compile chrono support as this just needs standard system libs.
+Also not sure why I was working on libdsol1-xml-java as it is not in Acacia and not needed.
+
+So, that should be it...
Added: trunk/packages/acacia/trunk/debian/acacia.desktop
===================================================================
--- trunk/packages/acacia/trunk/debian/acacia.desktop (rev 0)
+++ trunk/packages/acacia/trunk/debian/acacia.desktop 2014-04-10 13:18:12 UTC (rev 16651)
@@ -0,0 +1,12 @@
+[Desktop Entry]
+Version=1.0
+Type=Application
+Name=Acacia
+Comment=Correct errors in sequenced amplicons
+Exec=/usr/bin/acacia -u
+#Icon=/usr/share/pixmaps/acacia.png
+Icon=/usr/share/acacia/images/acacia_small_wattle_icon.png
+Terminal=false
+Categories=Science;Bioinformatics
+StartupNotify=true
+StartupWMClass=pyromaniac-AcaciaMain
Added: trunk/packages/acacia/trunk/debian/acacia.docs
===================================================================
--- trunk/packages/acacia/trunk/debian/acacia.docs (rev 0)
+++ trunk/packages/acacia/trunk/debian/acacia.docs 2014-04-10 13:18:12 UTC (rev 16651)
@@ -0,0 +1 @@
+README*
Added: trunk/packages/acacia/trunk/debian/acacia.install
===================================================================
--- trunk/packages/acacia/trunk/debian/acacia.install (rev 0)
+++ trunk/packages/acacia/trunk/debian/acacia.install 2014-04-10 13:18:12 UTC (rev 16651)
@@ -0,0 +1,4 @@
+src/data /usr/share/acacia
+src/images /usr/share/acacia
+debian/bin/* /usr/bin
+debian/*.desktop /usr/share/applications
Added: trunk/packages/acacia/trunk/debian/acacia.jlibs
===================================================================
--- trunk/packages/acacia/trunk/debian/acacia.jlibs (rev 0)
+++ trunk/packages/acacia/trunk/debian/acacia.jlibs 2014-04-10 13:18:12 UTC (rev 16651)
@@ -0,0 +1 @@
+acacia.jar
Added: trunk/packages/acacia/trunk/debian/bin/acacia
===================================================================
--- trunk/packages/acacia/trunk/debian/bin/acacia (rev 0)
+++ trunk/packages/acacia/trunk/debian/bin/acacia 2014-04-10 13:18:12 UTC (rev 16651)
@@ -0,0 +1,10 @@
+#!/bin/sh
+
+# Note the Acacia JAR provided in the Debian package has been rebuilt from
+# source and is much smaller than the one found on the Acacia website as it
+# does not contain all the dependencies within itself.
+
+# However, it should still run normally as the Manifest is set to load all the
+# dependencies from the files provided on the system.
+
+java -jar /usr/share/java/acacia.jar "$@"
Property changes on: trunk/packages/acacia/trunk/debian/bin/acacia
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/acacia/trunk/debian/changelog
===================================================================
--- trunk/packages/acacia/trunk/debian/changelog (rev 0)
+++ trunk/packages/acacia/trunk/debian/changelog 2014-04-10 13:18:12 UTC (rev 16651)
@@ -0,0 +1,6 @@
+acacia (1.53-0biolinux1) precise; urgency=low
+
+ * Initial release for Bio-Linux.
+ * Started with 1.52 but realised the later code is on GitHub.
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Fri, 04 Apr 2014 11:00:31 +0100
Added: trunk/packages/acacia/trunk/debian/classpath.sh
===================================================================
--- trunk/packages/acacia/trunk/debian/classpath.sh (rev 0)
+++ trunk/packages/acacia/trunk/debian/classpath.sh 2014-04-10 13:18:12 UTC (rev 16651)
@@ -0,0 +1,48 @@
+#!/bin/sh
+
+# Print the classpath. Simple.
+# Or else print a config for jh_manifest
+jars="
+ biojava1.7
+ ssj
+ optimization
+ colt
+ dsol-logger
+ dsol-event
+ dsol-interpreter
+ dsol-language
+ commons-cli
+ commons-math3
+ hac
+"
+
+mainclass="pyromaniac.AcaciaMain"
+
+if [ "$1" = -m ] ; then # manifest mode
+ echo "#Manifest generated by '$0 $@'"
+ echo
+ echo "usr/share/java/$2.jar:"
+ echo " Main-Class: $mainclass"
+ echo " Manifest-Version: 1.0"
+fi
+
+cp="$CLASSPATH"
+mcp=" /usr/share/acacia/"
+
+for c in $jars ; do
+ if [ "${c##/}" = "$c" ] ; then
+ f="/usr/share/java/$c.jar"
+ ls "$f" > /dev/null
+ cp="$cp:$f"
+ mcp="$mcp $c.jar"
+ else
+ cp="$cp:$c"
+ mcp="$mcp $c"
+ fi
+done
+
+if [ "$1" = -m ] ; then
+ echo " Class-Path:$mcp"
+else
+ echo ${cp##:}
+fi
Property changes on: trunk/packages/acacia/trunk/debian/classpath.sh
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/acacia/trunk/debian/compat
===================================================================
--- trunk/packages/acacia/trunk/debian/compat (rev 0)
+++ trunk/packages/acacia/trunk/debian/compat 2014-04-10 13:18:12 UTC (rev 16651)
@@ -0,0 +1 @@
+9
Added: trunk/packages/acacia/trunk/debian/control
===================================================================
--- trunk/packages/acacia/trunk/debian/control (rev 0)
+++ trunk/packages/acacia/trunk/debian/control 2014-04-10 13:18:12 UTC (rev 16651)
@@ -0,0 +1,32 @@
+Source: acacia
+Section: java
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Tim Booth <tbooth at ceh.ac.uk>
+DM-Upload-Allowed: yes
+Build-Depends: debhelper (>= 9), default-jdk, javahelper, libssj-java, libbiojava1.7-java,
+ libhac-java, libcommons-cli-java, libcommons-math3-java
+Standards-Version: 3.9.3
+Homepage: http://sourceforge.net/projects/acaciaerrorcorr/
+
+Package: acacia
+Architecture: all
+Depends: ${misc:Depends}, ${java:Depends}
+Description: Error-corrector for pyrosequenced amplicon reads.
+ Acacia is a java program developed to quickly and conservatively correct
+ errors, whilst simultaneously de-replicating, amplicon sequences.
+ .
+ The main purpose of Acacia is to correct the over-call, under-call errors
+ prevalent in Roche 454 GS-FLX data, and more recently, with the Titanium
+ chemistry.
+ Acacia will only ectively correct errors in amplicons - as it assumes that
+ the 5' end of the sequences start at the same position, the MID, followed by
+ the primer.
+ Acacia uses empirically-derived models to identify homopolymer
+ regions where there are more `errors' than expected by chance - these imply
+ that the differences are due to population differences rather than
+ error-induced polymorphisms.
+ .
+ Nat Methods. 2012 Apr 27;9(5):425-6. doi: 10.1038/nmeth.1990.
+ Fast, accurate error-correction of amplicon pyrosequences using Acacia.
+ Bragg L, Stone G, Imelfort M, Hugenholtz P, Tyson GW.
Added: trunk/packages/acacia/trunk/debian/copyright
===================================================================
--- trunk/packages/acacia/trunk/debian/copyright (rev 0)
+++ trunk/packages/acacia/trunk/debian/copyright 2014-04-10 13:18:12 UTC (rev 16651)
@@ -0,0 +1,25 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: acaciaerrorcorr
+Upstream-Contact: Lauren Bragg <lauren.bragg at csiro.au>
+Source: https://github.com/LBragg/Acacia
+
+Files: *
+Copyright: © 2011-2014 Lauren Bragg and Glenn Stone,
+ CSIRO CMIS & University of Queensland
+License: GPL-3
+ Acacia 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.
+ Acacia 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.
+ .
+ On Debian systems, the full text of the GNU General Public
+ License version 2 can be found in the file
+ `/usr/share/common-licenses/GPL-3'.
+
+
+Files: debian/*
+Copyright: © 2014 Tim Booth <tbooth at ceh.ac.uk>
+License: GPL-3
Added: trunk/packages/acacia/trunk/debian/rules
===================================================================
--- trunk/packages/acacia/trunk/debian/rules (rev 0)
+++ trunk/packages/acacia/trunk/debian/rules 2014-04-10 13:18:12 UTC (rev 16651)
@@ -0,0 +1,28 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+%:
+ dh $@ --with javahelper
+
+override_jh_manifest:
+ debian/classpath.sh -m acacia > debian/acacia.manifest
+ jh_manifest
+
+override_dh_auto_build:
+ env CLASSPATH=`debian/classpath.sh` jh_build acacia.jar src/pyromaniac
+
+override_dh_auto_clean:
+ find \( -name debian -prune \) -o -name '.?*' -prune -exec rm -rf '{}' ';'
+ find -name '*.zip' -delete
+ find -name '*.jar' -delete
+
+override_dh_clean:
+ dh_clean
+ #Remove auto-generated file
+ rm -f debian/acacia.manifest
+
+override_dh_compress:
+ dh_compress --exclude=.pdf
Property changes on: trunk/packages/acacia/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/acacia/trunk/debian/source/format
===================================================================
--- trunk/packages/acacia/trunk/debian/source/format (rev 0)
+++ trunk/packages/acacia/trunk/debian/source/format 2014-04-10 13:18:12 UTC (rev 16651)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/acacia/trunk/debian/watch
===================================================================
--- trunk/packages/acacia/trunk/debian/watch (rev 0)
+++ trunk/packages/acacia/trunk/debian/watch 2014-04-10 13:18:12 UTC (rev 16651)
@@ -0,0 +1,4 @@
+version=3
+# There is a source dump on SF.net but actually the latest code is on GitHub
+# https://github.com/LBragg/Acacia
+http://sf.net/acaciaerrorcorr/Acacia-([0-9.]+)_src.(?:tar.gz|.tar.bz2|.tgz)
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