Author: tbooth-guest
Date: 2015-01-19 14:49:28 +0000 (Mon, 19 Jan 2015)
New Revision: 18582
Added:
trunk/packages/librdp-alignment-java/trunk/debian/README.Debian
trunk/packages/librdp-alignment-java/trunk/debian/bin/
trunk/packages/librdp-alignment-java/trunk/debian/bin/rdp-alignment
trunk/packages/librdp-alignment-java/trunk/debian/changelog
trunk/packages/librdp-alignment-java/trunk/debian/compat
trunk/packages/librdp-alignment-java/trunk/debian/control
trunk/packages/librdp-alignment-java/trunk/debian/copyright
trunk/packages/librdp-alignment-java/trunk/debian/docs
trunk/packages/librdp-alignment-java/trunk/debian/install
trunk/packages/librdp-alignment-java/trunk/debian/jlibs
trunk/packages/librdp-alignment-java/trunk/debian/junit.xml
trunk/packages/librdp-alignment-java/trunk/debian/rules
trunk/packages/librdp-alignment-java/trunk/debian/source/
trunk/packages/librdp-alignment-java/trunk/debian/source/format
trunk/packages/librdp-alignment-java/trunk/debian/watch
Log:
Library needed for latest rdp-classifier
This probably needs updating - check GitHub
Added: trunk/packages/librdp-alignment-java/trunk/debian/README.Debian
===================================================================
--- trunk/packages/librdp-alignment-java/trunk/debian/README.Debian
(rev 0)
+++ trunk/packages/librdp-alignment-java/trunk/debian/README.Debian
2015-01-19 14:49:28 UTC (rev 18582)
@@ -0,0 +1,3 @@
+This package provides a convenience binary called "rdp-alignment" which is
equivalent to
+running "java -jar /path/to/AlignmentTools.jar" if you have built the JAR
following the upstream
+instructions.
Added: trunk/packages/librdp-alignment-java/trunk/debian/bin/rdp-alignment
===================================================================
--- trunk/packages/librdp-alignment-java/trunk/debian/bin/rdp-alignment
(rev 0)
+++ trunk/packages/librdp-alignment-java/trunk/debian/bin/rdp-alignment
2015-01-19 14:49:28 UTC (rev 18582)
@@ -0,0 +1,3 @@
+#!/bin/sh
+
+exec java -jar /usr/share/java/rdp-alignment.jar "$@"
Added: trunk/packages/librdp-alignment-java/trunk/debian/changelog
===================================================================
--- trunk/packages/librdp-alignment-java/trunk/debian/changelog
(rev 0)
+++ trunk/packages/librdp-alignment-java/trunk/debian/changelog 2015-01-19
14:49:28 UTC (rev 18582)
@@ -0,0 +1,5 @@
+librdp-alignment-java (0.1.20140606-0biolinux1) trusty; urgency=medium
+
+ * New package wanted for rdp-classifier
+
+ -- Tim Booth <[email protected]> Mon, 06 Oct 2014 18:14:33 +0100
Added: trunk/packages/librdp-alignment-java/trunk/debian/compat
===================================================================
--- trunk/packages/librdp-alignment-java/trunk/debian/compat
(rev 0)
+++ trunk/packages/librdp-alignment-java/trunk/debian/compat 2015-01-19
14:49:28 UTC (rev 18582)
@@ -0,0 +1 @@
+9
Added: trunk/packages/librdp-alignment-java/trunk/debian/control
===================================================================
--- trunk/packages/librdp-alignment-java/trunk/debian/control
(rev 0)
+++ trunk/packages/librdp-alignment-java/trunk/debian/control 2015-01-19
14:49:28 UTC (rev 18582)
@@ -0,0 +1,17 @@
+Source: librdp-alignment-java
+Section: java
+Priority: extra
+Maintainer: Tim Booth <[email protected]>
+Build-Depends: debhelper (>= 9), default-jdk, javahelper, libcommons-io-java,
+ libcommons-cli-java, libcommons-lang-java, junit4, ant,
ant-optional,
+ librdp-readseq-java ( >= 0.1.20140922)
+Standards-Version: 3.9.3
+
+Package: librdp-alignment-java
+Architecture: all
+Depends: ${shlibs:Depends}, ${misc:Depends}, ${java:Depends}
+Description: RDP Alignment tools package
+ The Alignment tools package contains commands to do defined community analysis
+ (Fish et al., 2013. FunGene: the functional gene pipeline and repository.
+ Frontiers, Accepted), pairwise alignment and hidden markov model
+ (HMMER3 models, no training).
Added: trunk/packages/librdp-alignment-java/trunk/debian/copyright
===================================================================
--- trunk/packages/librdp-alignment-java/trunk/debian/copyright
(rev 0)
+++ trunk/packages/librdp-alignment-java/trunk/debian/copyright 2015-01-19
14:49:28 UTC (rev 18582)
@@ -0,0 +1,14 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: rdpstaff/AlignmentTools
+Upstream-Contact: https://github.com/wangqion
+Source: https://github.com/rdpstaff/AlignmentTools/commits/master
+
+Files: *
+Copyright: Copyright (C) 2014 Michigan State University <[email protected]>
+License: GPL-3
+ On Debian systems, you can read the full text of the GNU General Public
+ License in ‘/usr/share/common-licenses/GPL-3’.
+
+Files: debian/*
+Copyright: © Tim Booth <[email protected]>
+License: GPL-3
Added: trunk/packages/librdp-alignment-java/trunk/debian/docs
===================================================================
--- trunk/packages/librdp-alignment-java/trunk/debian/docs
(rev 0)
+++ trunk/packages/librdp-alignment-java/trunk/debian/docs 2015-01-19
14:49:28 UTC (rev 18582)
@@ -0,0 +1 @@
+README.md
Added: trunk/packages/librdp-alignment-java/trunk/debian/install
===================================================================
--- trunk/packages/librdp-alignment-java/trunk/debian/install
(rev 0)
+++ trunk/packages/librdp-alignment-java/trunk/debian/install 2015-01-19
14:49:28 UTC (rev 18582)
@@ -0,0 +1 @@
+debian/bin/* /usr/bin
Added: trunk/packages/librdp-alignment-java/trunk/debian/jlibs
===================================================================
--- trunk/packages/librdp-alignment-java/trunk/debian/jlibs
(rev 0)
+++ trunk/packages/librdp-alignment-java/trunk/debian/jlibs 2015-01-19
14:49:28 UTC (rev 18582)
@@ -0,0 +1 @@
+*.jar
Added: trunk/packages/librdp-alignment-java/trunk/debian/junit.xml
===================================================================
--- trunk/packages/librdp-alignment-java/trunk/debian/junit.xml
(rev 0)
+++ trunk/packages/librdp-alignment-java/trunk/debian/junit.xml 2015-01-19
14:49:28 UTC (rev 18582)
@@ -0,0 +1,22 @@
+<!-- Snippet to drive junit tests in deb build. Build rdp-alignment.jar first
and ensure
+ it depends on rdp-readseq.jar (jh should take care of that). -->
+<project>
+<target name="junit">
+
+ <property name="cp"
value="/usr/share/java/commons-cli.jar:/usr/share/java/commons-lang.jar:/usr/share/java/commons-io.jar:rdp-alignment.jar:/usr/share/java/junit4.jar:test"/>
+
+ <javac srcdir="test">
+ <classpath path="${cp}"/>
+ </javac>
+
+ <junit printsummary="yes" haltonfailure="yes" showoutput="yes">
+ <classpath path="${cp}"/>
+
+ <formatter type="xml"/>
+
+ <batchtest fork="yes">
+ <fileset dir="test" includes="**/*Test.java"/>
+ </batchtest>
+ </junit>
+</target>
+</project>
Added: trunk/packages/librdp-alignment-java/trunk/debian/rules
===================================================================
--- trunk/packages/librdp-alignment-java/trunk/debian/rules
(rev 0)
+++ trunk/packages/librdp-alignment-java/trunk/debian/rules 2015-01-19
14:49:28 UTC (rev 18582)
@@ -0,0 +1,33 @@
+#!/usr/bin/make -f
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+export
CLASSPATH=/usr/share/java/commons-cli.jar:/usr/share/java/commons-lang.jar:/usr/share/java/commons-io.jar:/usr/share/java/rdp-readseq.jar
+
+%:
+ dh $@ --with javahelper
+
+override_dh_auto_clean:
+ rm -rf lib build *.jar junit-tmp.xml TEST-*.xml
+ find test -name '*.class' -delete
+
+override_dh_auto_test:
+ cp debian/junit.xml ./junit-tmp.xml
+ ant -f junit-tmp.xml junit
+
+override_dh_clean:
+ dh_clean
+ rm -f debian/manifest
+ rm -f debian/*.log
+
+override_dh_auto_build:
+ #Ant is over-complicating things. Do it the easy way.
+ jh_build rdp-alignment.jar src
+ cd src ; jar uf ../rdp-alignment.jar data
+ #Also set the manifest like so
+ echo usr/share/java/rdp-alignment.jar: >debian/manifest
+ echo '\tClass-Path: commons-cli.jar commons-lang.jar commons-io.jar
rdp-readseq.jar' >>debian/manifest
+ echo '\tMain-Class: '`grep '^main.class=' nbproject/project.properties
| cut -c 12-` >>debian/manifest
+
+
Property changes on: trunk/packages/librdp-alignment-java/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/librdp-alignment-java/trunk/debian/source/format
===================================================================
--- trunk/packages/librdp-alignment-java/trunk/debian/source/format
(rev 0)
+++ trunk/packages/librdp-alignment-java/trunk/debian/source/format
2015-01-19 14:49:28 UTC (rev 18582)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/librdp-alignment-java/trunk/debian/watch
===================================================================
--- trunk/packages/librdp-alignment-java/trunk/debian/watch
(rev 0)
+++ trunk/packages/librdp-alignment-java/trunk/debian/watch 2015-01-19
14:49:28 UTC (rev 18582)
@@ -0,0 +1,4 @@
+# Compulsory line, this is a version 3 file
+version=3
+
+# I had to get this manually off GitHub, and base the version on the last
commit date.
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