[med-svn] [proalign] 02/10: proalign almost ready, just needs a manpage and some tests

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository proalign.

commit 7c24863b5060c56ac66ae72795d39a5742ed5f43
Author: Thorsten Alteholz <alteholz at debian.org>
Date:   Wed May 1 20:09:53 2013 +0000

    proalign almost ready, just needs a manpage and some tests
---
 debian/changelog        |  4 ++--
 debian/control          |  9 +++++----
 debian/manifest.txt     |  3 +++
 debian/proalign.install |  3 +++
 debian/rules            | 23 +++++++++++++++++++++++
 debian/scripts/proalign | 19 +++++++++++++++++++
 debian/source/format    |  1 +
 debian/watch            |  2 +-
 8 files changed, 57 insertions(+), 7 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 231d26a..77940b8 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,5 +1,5 @@
-proalign (0.603-1) unstable; urgency=low
+proalign (0.603-1) UNRELEASED; urgency=low
 
   * Initial release (Closes: #378290)
 
- -- Andreas Tille <tille at debian.org>  Thu, 24 May 2012 14:30:13 +0200
+ -- Thorsten Alteholz <debian at alteholz.de>  Tue, 01 May 2013 18:00:00 +0200
diff --git a/debian/control b/debian/control
index a42d0a6..8f03506 100644
--- a/debian/control
+++ b/debian/control
@@ -3,9 +3,10 @@ Section: science
 Priority: optional
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 DM-Upload-Allowed: yes
-Uploaders: Andreas Tille <tille at debian.org>
+Uploaders: Andreas Tille <tille at debian.org>,
+ Thorsten Alteholz <debian at alteholz.de>
 Build-Depends: debhelper (>= 9)
-Standards-Version: 3.9.3
+Standards-Version: 3.9.4
 Homepage: http://ueg.ulb.ac.be/ProAlign/
 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/proalign/trunk/
 Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/proalign/trunk/
@@ -18,11 +19,11 @@ Description: Probabilistic multiple alignment program
  models (HMM). It includes a graphical interface (GUI) allowing to (i)
  perform alignments of nucleotide or amino-acid sequences, (ii) view the
  quality of solutions, (iii) filter the unreliable alignment regions and
- (iv) export alignments to other softwares.
+ (iv) export alignments to other software.
  .
  ProAlign uses a progressive method, such that multiple alignment is
  created stepwise by performing pairwise alignments in the nodes of a
  guide tree. Sequences are described with vectors of character
  probabilities, and each pairwise alignment reconstructs the ancestral
  (parent) sequence by computing the probabilities of different
- characters according to an evolutionary model.
\ No newline at end of file
+ characters according to an evolutionary model.
diff --git a/debian/manifest.txt b/debian/manifest.txt
new file mode 100644
index 0000000..3497d16
--- /dev/null
+++ b/debian/manifest.txt
@@ -0,0 +1,3 @@
+Manifest-version: 1.0
+Main-Class: proalign.ProAlign
+
diff --git a/debian/proalign.install b/debian/proalign.install
new file mode 100644
index 0000000..32cb5c6
--- /dev/null
+++ b/debian/proalign.install
@@ -0,0 +1,3 @@
+debian/scripts/proalign usr/bin
+build/ProAlign.jar usr/share/proalign
+
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..1d3af7e
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,23 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+
+%:
+	dh $@
+
+override_dh_auto_build:
+	mkdir -p build
+	javac -d ./build *.java
+	find
+	(cd build; jar cmvf ../debian/manifest.txt ProAlign.jar *)
+	#(cd build; jar cmvf ../debian/manifest.txt ProAlign.jar proalign/ProAlign.class proalign/OutFile.class)
+
+override_dh_auto_install:
+	find
+	dh_auto_install
+	#dh_installchangelogs README
+
+get-orig-source:
+	mkdir -p ../tarballs
+	uscan --verbose --force-download --destdir=../tarballs
+
diff --git a/debian/scripts/proalign b/debian/scripts/proalign
new file mode 100644
index 0000000..474feb7
--- /dev/null
+++ b/debian/scripts/proalign
@@ -0,0 +1,19 @@
+#!/bin/sh
+
+if [ -z $JAVA_HOME ]; then
+        java=java
+else
+        java=$JAVA_HOME/bin/java
+fi
+
+if [ -x /usr/share/proalign ]; then
+        if [ -r /usr/share/proalign/ProAlign.jar  ]; then 
+                #cd /usr/share/proalign && $java -jar ProAlign.jar
+                $java -jar /usr/share/proalign/ProAlign.jar
+        else 
+                echo "Could not find /usr/share/proalign/ProAlign.jar"
+        fi
+else 
+        echo "Could not find /usr/share/proalign directory."
+fi
+
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/watch b/debian/watch
index de887af..a743fa0 100644
--- a/debian/watch
+++ b/debian/watch
@@ -1,4 +1,4 @@
 version=3
 
-opts=dversionmangle=s/\.// \
+opts=uversionmangle=s/0/0\./ \
   http://ueg.ulb.ac.be/ProAlign/download/src/proalign_(.+)\.tgz

-- 
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