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