[med-svn] [jaligner] 01/01: initial debianization

[Timothy Booth]

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

tbooth-guest pushed a commit to branch master
in repository jaligner.

commit 3c17c9180ceebcec4235f9ce9fb426080da5193f
Author: Tim Booth <tbooth at ceh.ac.uk>
Date:   Sun Feb 1 18:53:41 2015 +0000

    initial debianization
---
 debian/bin/jaligner  |  3 +++
 debian/changelog     |  5 +++++
 debian/compat        |  1 +
 debian/control       | 15 +++++++++++++++
 debian/install       |  1 +
 debian/jlibs         |  1 +
 debian/manifest      |  4 ++++
 debian/rules         | 20 ++++++++++++++++++++
 debian/source/format |  1 +
 9 files changed, 51 insertions(+)

diff --git a/debian/bin/jaligner b/debian/bin/jaligner
new file mode 100755
index 0000000..8ed6f78
--- /dev/null
+++ b/debian/bin/jaligner
@@ -0,0 +1,3 @@
+#!/bin/sh
+
+exec java -Xms128m -Xmx512m -jar /usr/share/java/jaligner.jar "$@"
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..208da31
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+jaligner (1.0) trusty; urgency=medium
+
+  * Initial release. (Closes: #XXXXXX)
+
+ -- Tim Booth <tbooth at ceh.ac.uk>  Sun, 01 Feb 2015 17:30:31 +0000
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..45a4fb7
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+8
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..e27e1cd
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,15 @@
+Source: jaligner
+Section: science
+Priority: extra
+Maintainer: Tim Booth <tbooth at ceh.ac.uk>
+Build-Depends: debhelper (>= 9), default-jdk, junit4, javahelper,
+               icedtea-netx-common
+Standards-Version: 3.9.5
+
+Package: jaligner
+Architecture: all
+Depends: ${java:Depends}, ${misc:Depends}, default-jre
+Description: implementation of the Smith-Waterman algorithm with Gotoh's improvement
+ JAligner is an open source Java implementation of the Smith-Waterman
+ algorithm with Gotoh's improvement for biological local pairwise sequence
+ alignment with the affine gap penalty model.
diff --git a/debian/install b/debian/install
new file mode 100644
index 0000000..3501fc5
--- /dev/null
+++ b/debian/install
@@ -0,0 +1 @@
+debian/bin/* /usr/bin/
diff --git a/debian/jlibs b/debian/jlibs
new file mode 100644
index 0000000..c8c90c6
--- /dev/null
+++ b/debian/jlibs
@@ -0,0 +1 @@
+jaligner.jar
diff --git a/debian/manifest b/debian/manifest
new file mode 100644
index 0000000..45cda57
--- /dev/null
+++ b/debian/manifest
@@ -0,0 +1,4 @@
+usr/share/java/jaligner.jar:
+    Main-Class: jaligner.ui.AlignCommandLine
+    Manifest-Version: 1.0
+    Class-Path: /usr/share/jaligner/
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..01cb00c
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,20 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+export CLASSPATH=/usr/share/icedtea-web/netx.jar
+
+%:
+	dh $@ --with javahelper
+
+override_dh_auto_build:
+	jh_build -J jaligner.jar src
+
+override_dh_install:
+	dh_install src/jaligner /usr/share/jaligner
+	find debian/jaligner/usr/share/jaligner -type f -a \( -name '*.java' -o -name '*.html' \) -delete
+
+override_dh_auto_clean:
+	rm -f jaligner.jar
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)

-- 
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