[med-svn] r12045 - in trunk/packages/rdp-classifier/trunk/debian: . scripts
Timothy Booth
tbooth-guest at alioth.debian.org
Tue Aug 14 16:49:40 UTC 2012
Author: tbooth-guest
Date: 2012-08-14 16:49:39 +0000 (Tue, 14 Aug 2012)
New Revision: 12045
Added:
trunk/packages/rdp-classifier/trunk/debian/MANIFEST.MF
trunk/packages/rdp-classifier/trunk/debian/rdp-classifier-doc.install
trunk/packages/rdp-classifier/trunk/debian/rdp-classifier.install
trunk/packages/rdp-classifier/trunk/debian/scripts/
trunk/packages/rdp-classifier/trunk/debian/scripts/rdp_classifier
Removed:
trunk/packages/rdp-classifier/trunk/debian/install
Modified:
trunk/packages/rdp-classifier/trunk/debian/README.source
trunk/packages/rdp-classifier/trunk/debian/changelog
trunk/packages/rdp-classifier/trunk/debian/control
trunk/packages/rdp-classifier/trunk/debian/copyright
trunk/packages/rdp-classifier/trunk/debian/rdp-classifier.docs
trunk/packages/rdp-classifier/trunk/debian/rules
Log:
I think this is everything I need to get it working properly.
Still no reply regarding the missing source but we live in hope.
Added: trunk/packages/rdp-classifier/trunk/debian/MANIFEST.MF
===================================================================
--- trunk/packages/rdp-classifier/trunk/debian/MANIFEST.MF (rev 0)
+++ trunk/packages/rdp-classifier/trunk/debian/MANIFEST.MF 2012-08-14 16:49:39 UTC (rev 12045)
@@ -0,0 +1,5 @@
+X-COMMENT: Manifest made by Tim Booth for Debian packaging
+Manifest-Version: 1.0
+Class-Path: /usr/share/java/commons-cli.jar ./ReadSeq.jar /usr/share/java/junit.jar
+Main-Class: edu.msu.cme.rdp.classifier.ClassifierCmd
+
Modified: trunk/packages/rdp-classifier/trunk/debian/README.source
===================================================================
--- trunk/packages/rdp-classifier/trunk/debian/README.source 2012-08-14 12:32:55 UTC (rev 12044)
+++ trunk/packages/rdp-classifier/trunk/debian/README.source 2012-08-14 16:49:39 UTC (rev 12045)
@@ -10,4 +10,7 @@
have made a package that builds using the pre-compiled ReadSeq.jar. This could go
into non-free.
(Note that having the package like this contravenes the SourceForge TOS so the
-authro is very naughty!)
+author is very naughty!)
+
+I also noticed that Steffen started packaging this as a Java library, but I think it's
+a Java application.
Modified: trunk/packages/rdp-classifier/trunk/debian/changelog
===================================================================
--- trunk/packages/rdp-classifier/trunk/debian/changelog 2012-08-14 12:32:55 UTC (rev 12044)
+++ trunk/packages/rdp-classifier/trunk/debian/changelog 2012-08-14 16:49:39 UTC (rev 12045)
@@ -1,8 +1,12 @@
-rdp-classifier (2.5.0-1) precise; urgency=low
+rdp-classifier (2.5+repack-2) precise; urgency=low
* Rebuild version 2.5 (for Ubuntu)
+ * Try to do proper build but there is missing source! - see README.source
+ * Make use of JavaHelper for deps
+ * Add wrapper script in /usr/bin to run the app (from BL)
+ * Split out separate -doc package
- -- Tim Booth <tbooth at ceh.ac.uk> Mon, 13 Aug 2012 16:11:15 +0100
+ -- Tim Booth <tbooth at ceh.ac.uk> Tue, 14 Aug 2012 17:30:11 +0100
rdp-classifier (2.0.1-1) UNRELEASED; urgency=low
Modified: trunk/packages/rdp-classifier/trunk/debian/control
===================================================================
--- trunk/packages/rdp-classifier/trunk/debian/control 2012-08-14 12:32:55 UTC (rev 12044)
+++ trunk/packages/rdp-classifier/trunk/debian/control 2012-08-14 16:49:39 UTC (rev 12045)
@@ -2,16 +2,26 @@
Section: science
Priority: extra
Maintainer: Steffen Moeller <steffen_moeller at gmx.de>
-Build-Depends: debhelper (>= 7.0.50~), default-jdk, junit, libcommons-cli-java
-Standards-Version: 3.9.4
+Uploaders: Tim Booth <tbooth at ceh.ac.uk>
+Build-Depends: debhelper (>= 7.0.50~), default-jdk, junit, libcommons-cli-java, javahelper
+Standards-Version: 3.9.3
Homepage: http://rdp.cme.msu.edu/.
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/rdp-classifier/trunk/
Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/rdp-classifier/trunk/
Package: rdp-classifier
Architecture: all
-Depends: ${shlibs:Depends}, ${misc:Depends}, default-jre
+Depends: ${java:Depends}, ${misc:Depends}, default-jre
+Recommends: rdp-classifier-doc
Description: taxonomic assignment from next generation sequencing
The RDP Classifier is a nave Bayesian classifier that can rapidly and
accurately provides taxonomic assignments from domain to genus, with
confidence estimates for each assignment.
+
+Package: rdp-classifier-doc
+Architecture: all
+Section: doc
+Depends: ${misc:Depends}
+Suggests: rdp-classifier
+Description: documentation and examples for rdp-classifier
+ Includes the JavaDoc HTML
Modified: trunk/packages/rdp-classifier/trunk/debian/copyright
===================================================================
--- trunk/packages/rdp-classifier/trunk/debian/copyright 2012-08-14 12:32:55 UTC (rev 12044)
+++ trunk/packages/rdp-classifier/trunk/debian/copyright 2012-08-14 16:49:39 UTC (rev 12045)
@@ -1,9 +1,9 @@
Format: http://dep.debian.net/deps/dep5
Upstream-Name: rdp-classifier
-Source: http://downloads.sourceforge.net/project/rdp-classifier/rdp-classifier/rdp_classifier_2.0.1/rdp_classifier_2.0.1.tar.gz
+Source: http://downloads.sourceforge.net/project/rdp-classifier/
Files: *
-Copyright: 2008 Michigan State University Board of Trustees
+Copyright: 2008-2012 Michigan State University Board of Trustees
James R. Cole <colej at msu.edu>
Qiong Wang <wangqion at msu.edu>
George M. Garrity <garrity at msu.edu>
Deleted: trunk/packages/rdp-classifier/trunk/debian/install
===================================================================
--- trunk/packages/rdp-classifier/trunk/debian/install 2012-08-14 12:32:55 UTC (rev 12044)
+++ trunk/packages/rdp-classifier/trunk/debian/install 2012-08-14 16:49:39 UTC (rev 12045)
@@ -1 +0,0 @@
-rdp_classifier*.jar usr/share/java
Added: trunk/packages/rdp-classifier/trunk/debian/rdp-classifier-doc.install
===================================================================
--- trunk/packages/rdp-classifier/trunk/debian/rdp-classifier-doc.install (rev 0)
+++ trunk/packages/rdp-classifier/trunk/debian/rdp-classifier-doc.install 2012-08-14 16:49:39 UTC (rev 12045)
@@ -0,0 +1 @@
+docs /usr/share/doc/rdp-classifier/
Modified: trunk/packages/rdp-classifier/trunk/debian/rdp-classifier.docs
===================================================================
--- trunk/packages/rdp-classifier/trunk/debian/rdp-classifier.docs 2012-08-14 12:32:55 UTC (rev 12044)
+++ trunk/packages/rdp-classifier/trunk/debian/rdp-classifier.docs 2012-08-14 16:49:39 UTC (rev 12045)
@@ -1,2 +1 @@
README
-docs
Copied: trunk/packages/rdp-classifier/trunk/debian/rdp-classifier.install (from rev 12039, trunk/packages/rdp-classifier/trunk/debian/install)
===================================================================
--- trunk/packages/rdp-classifier/trunk/debian/rdp-classifier.install (rev 0)
+++ trunk/packages/rdp-classifier/trunk/debian/rdp-classifier.install 2012-08-14 16:49:39 UTC (rev 12045)
@@ -0,0 +1,3 @@
+rdp_classifier.jar usr/share/rdp-classifier
+lib/ReadSeq.jar usr/share/rdp-classifier
+debian/scripts/rdp_classifier usr/bin
Modified: trunk/packages/rdp-classifier/trunk/debian/rules
===================================================================
--- trunk/packages/rdp-classifier/trunk/debian/rules 2012-08-14 12:32:55 UTC (rev 12044)
+++ trunk/packages/rdp-classifier/trunk/debian/rules 2012-08-14 16:49:39 UTC (rev 12045)
@@ -12,15 +12,16 @@
CP=/usr/share/java/junit.jar:/usr/share/java/commons-cli.jar
%:
- dh $@
+ dh $@ --with javahelper
override_dh_auto_build:
##NR## - should not be using binary JAR in build
javac -cp ${CP}:lib/ReadSeq.jar `find ${SRC} -name "*.java" -and -not -name "._*"`
( cd ${SRC} ; find . -name "*.class" ) > rdp_classifier.list
- ( cd ${SRC} ; jar -c @/dev/stdin data ) < rdp_classifier.list > rdp_classifier.jar
+ ( cd ${SRC} ; jar -mc ${CURDIR}/debian/MANIFEST.MF @${CURDIR}/rdp_classifier.list data ) > rdp_classifier.jar
override_dh_auto_clean:
find . -name "*.class" | xargs -r rm -f
##NR## rm -f "*.jar" lib/*.jar
+ rm -f rdp_classifier.jar
rm -f *.list
Added: trunk/packages/rdp-classifier/trunk/debian/scripts/rdp_classifier
===================================================================
--- trunk/packages/rdp-classifier/trunk/debian/scripts/rdp_classifier (rev 0)
+++ trunk/packages/rdp-classifier/trunk/debian/scripts/rdp_classifier 2012-08-14 16:49:39 UTC (rev 12045)
@@ -0,0 +1,10 @@
+#!/bin/sh
+
+# Note that the JAR MANIFEST points to the locations of the
+# required libs on Debian so no setting of Classpath is needed here.
+# For the same reason, the JAR form this package is not going to be
+# happy running outside Debian.
+
+JAR=/usr/share/rdp-classifier/rdp_classifier.jar
+
+exec java -Xms512M -Xmx512M -jar "$JAR" "$@"
Property changes on: trunk/packages/rdp-classifier/trunk/debian/scripts/rdp_classifier
___________________________________________________________________
Added: svn:executable
+ *
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