[med-svn] r18581 - in trunk/packages/librdp-readseq-java/trunk/debian: . bin source
Timothy Booth
tbooth-guest at moszumanska.debian.org
Mon Jan 19 14:46:20 UTC 2015
Author: tbooth-guest
Date: 2015-01-19 14:46:19 +0000 (Mon, 19 Jan 2015)
New Revision: 18581
Added:
trunk/packages/librdp-readseq-java/trunk/debian/README.Debian
trunk/packages/librdp-readseq-java/trunk/debian/bin/
trunk/packages/librdp-readseq-java/trunk/debian/bin/rdp-readseq
trunk/packages/librdp-readseq-java/trunk/debian/changelog
trunk/packages/librdp-readseq-java/trunk/debian/compat
trunk/packages/librdp-readseq-java/trunk/debian/control
trunk/packages/librdp-readseq-java/trunk/debian/copyright
trunk/packages/librdp-readseq-java/trunk/debian/docs
trunk/packages/librdp-readseq-java/trunk/debian/install
trunk/packages/librdp-readseq-java/trunk/debian/jlibs
trunk/packages/librdp-readseq-java/trunk/debian/junit.xml
trunk/packages/librdp-readseq-java/trunk/debian/manifest
trunk/packages/librdp-readseq-java/trunk/debian/rules
trunk/packages/librdp-readseq-java/trunk/debian/source/
trunk/packages/librdp-readseq-java/trunk/debian/source/format
trunk/packages/librdp-readseq-java/trunk/debian/watch
Log:
Lib needed by newest RDP-classifier
This is probably already out of date - check uscan
Added: trunk/packages/librdp-readseq-java/trunk/debian/README.Debian
===================================================================
--- trunk/packages/librdp-readseq-java/trunk/debian/README.Debian (rev 0)
+++ trunk/packages/librdp-readseq-java/trunk/debian/README.Debian 2015-01-19 14:46:19 UTC (rev 18581)
@@ -0,0 +1,3 @@
+This package provides a convenience binary called "rdp-readseq" which is equivalent to
+running "java -jar dist/ReadSeq.jar" if you have built the JAR following the upstream
+instructions.
Added: trunk/packages/librdp-readseq-java/trunk/debian/bin/rdp-readseq
===================================================================
--- trunk/packages/librdp-readseq-java/trunk/debian/bin/rdp-readseq (rev 0)
+++ trunk/packages/librdp-readseq-java/trunk/debian/bin/rdp-readseq 2015-01-19 14:46:19 UTC (rev 18581)
@@ -0,0 +1,3 @@
+#!/bin/sh
+
+exec java -jar /usr/share/java/rdp-readseq.jar "$@"
Added: trunk/packages/librdp-readseq-java/trunk/debian/changelog
===================================================================
--- trunk/packages/librdp-readseq-java/trunk/debian/changelog (rev 0)
+++ trunk/packages/librdp-readseq-java/trunk/debian/changelog 2015-01-19 14:46:19 UTC (rev 18581)
@@ -0,0 +1,11 @@
+librdp-readseq-java (0.1.20140922-0biolinux1) trusty; urgency=medium
+
+ * New upstream for rdp-classifier2.9
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Mon, 06 Oct 2014 18:14:33 +0100
+
+librdp-readseq-java (0.1.20140425-0biolinux2) trusty; urgency=low
+
+ * Initial package to help rdp-classifier
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Wed, 30 Apr 2014 18:16:24 +0100
Added: trunk/packages/librdp-readseq-java/trunk/debian/compat
===================================================================
--- trunk/packages/librdp-readseq-java/trunk/debian/compat (rev 0)
+++ trunk/packages/librdp-readseq-java/trunk/debian/compat 2015-01-19 14:46:19 UTC (rev 18581)
@@ -0,0 +1 @@
+9
Added: trunk/packages/librdp-readseq-java/trunk/debian/control
===================================================================
--- trunk/packages/librdp-readseq-java/trunk/debian/control (rev 0)
+++ trunk/packages/librdp-readseq-java/trunk/debian/control 2015-01-19 14:46:19 UTC (rev 18581)
@@ -0,0 +1,19 @@
+Source: librdp-readseq-java
+Section: java
+Priority: extra
+Maintainer: Tim Booth <tbooth at ceh.ac.uk>
+Build-Depends: debhelper (>= 9), default-jdk, javahelper, libcommons-io-java,
+ libcommons-cli-java, libcommons-lang-java, junit4, ant, ant-optional
+Standards-Version: 3.9.3
+
+Package: librdp-readseq-java
+Architecture: all
+Depends: ${shlibs:Depends}, ${misc:Depends}, ${java:Depends}
+Description: RDP sequence reading and writing library
+ Sequence reading library developed by the Ribosomal Database Project. Can
+ handle genbank, embl, fasta, fastq, sff and sto files. Can read from files
+ or streams, and can handle indexing files.
+ .
+ A basic rdp-readseq command line program is also included.
+ .
+ The ReadSeq project is a library used by other RDP tools
Added: trunk/packages/librdp-readseq-java/trunk/debian/copyright
===================================================================
--- trunk/packages/librdp-readseq-java/trunk/debian/copyright (rev 0)
+++ trunk/packages/librdp-readseq-java/trunk/debian/copyright 2015-01-19 14:46:19 UTC (rev 18581)
@@ -0,0 +1,16 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: rdpstaff/ReadSeq
+Upstream-Contact: https://github.com/wangqion
+Source: https://github.com/rdpstaff/ReadSeq/commits/master
+
+Files: *
+Copyright: Copyright (C) 2006-2012 Michigan State University <rdpstaff at msu.edu>,
+ 2012 Jordan Fish <fishjord at msu.edu>,
+ 2014 Qiong Wang <wangqion at msu.edu>
+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 <tbooth at ceh.ac.uk>
+License: GPL-3
Added: trunk/packages/librdp-readseq-java/trunk/debian/docs
===================================================================
--- trunk/packages/librdp-readseq-java/trunk/debian/docs (rev 0)
+++ trunk/packages/librdp-readseq-java/trunk/debian/docs 2015-01-19 14:46:19 UTC (rev 18581)
@@ -0,0 +1 @@
+README
Added: trunk/packages/librdp-readseq-java/trunk/debian/install
===================================================================
--- trunk/packages/librdp-readseq-java/trunk/debian/install (rev 0)
+++ trunk/packages/librdp-readseq-java/trunk/debian/install 2015-01-19 14:46:19 UTC (rev 18581)
@@ -0,0 +1 @@
+debian/bin/* /usr/bin
Added: trunk/packages/librdp-readseq-java/trunk/debian/jlibs
===================================================================
--- trunk/packages/librdp-readseq-java/trunk/debian/jlibs (rev 0)
+++ trunk/packages/librdp-readseq-java/trunk/debian/jlibs 2015-01-19 14:46:19 UTC (rev 18581)
@@ -0,0 +1 @@
+*.jar
Added: trunk/packages/librdp-readseq-java/trunk/debian/junit.xml
===================================================================
--- trunk/packages/librdp-readseq-java/trunk/debian/junit.xml (rev 0)
+++ trunk/packages/librdp-readseq-java/trunk/debian/junit.xml 2015-01-19 14:46:19 UTC (rev 18581)
@@ -0,0 +1,21 @@
+<!-- Snippet to drive junit tests in deb build. Build rdp-readseq.jar first. -->
+<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-readseq.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-readseq-java/trunk/debian/manifest
===================================================================
--- trunk/packages/librdp-readseq-java/trunk/debian/manifest (rev 0)
+++ trunk/packages/librdp-readseq-java/trunk/debian/manifest 2015-01-19 14:46:19 UTC (rev 18581)
@@ -0,0 +1,3 @@
+usr/share/java/rdp-readseq.jar:
+ Class-Path: commons-cli.jar commons-lang.jar commons-io.jar
+ Main-Class: edu.msu.cme.rdp.readseq.ReadSeqMain
Added: trunk/packages/librdp-readseq-java/trunk/debian/rules
===================================================================
--- trunk/packages/librdp-readseq-java/trunk/debian/rules (rev 0)
+++ trunk/packages/librdp-readseq-java/trunk/debian/rules 2015-01-19 14:46:19 UTC (rev 18581)
@@ -0,0 +1,25 @@
+#!/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
+
+%:
+ 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/*.log
+
+override_dh_auto_build:
+ jh_build rdp-readseq.jar src
+ cd src ; jar uf ../rdp-readseq.jar data
Property changes on: trunk/packages/librdp-readseq-java/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/librdp-readseq-java/trunk/debian/source/format
===================================================================
--- trunk/packages/librdp-readseq-java/trunk/debian/source/format (rev 0)
+++ trunk/packages/librdp-readseq-java/trunk/debian/source/format 2015-01-19 14:46:19 UTC (rev 18581)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/librdp-readseq-java/trunk/debian/watch
===================================================================
--- trunk/packages/librdp-readseq-java/trunk/debian/watch (rev 0)
+++ trunk/packages/librdp-readseq-java/trunk/debian/watch 2015-01-19 14:46:19 UTC (rev 18581)
@@ -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.
More information about the debian-med-commit
mailing list