[Debian-med-packaging] [SCM] igv branch, master, updated. upstream/1.4.2-2-g76d2507
Shaun Jackman
sjackman at debian.org
Wed Jun 16 01:08:48 UTC 2010
The following commit has been merged in the master branch:
commit 3a1a3119c481cd02efbedfb2210a3b9b93b7faf0
Author: Shaun Jackman <sjackman at debian.org>
Date: Tue Jun 15 18:04:53 2010 -0700
Initial release.
diff --git a/debian/README.source b/debian/README.source
new file mode 100644
index 0000000..0ca6b78
--- /dev/null
+++ b/debian/README.source
@@ -0,0 +1,4 @@
+Binary files in lib/* and native/* have been removed from the original
+upstream source.
+
+ -- Shaun Jackman <sjackman at debian.org> 2010-06-10
diff --git a/debian/bin/igv b/debian/bin/igv
new file mode 100644
index 0000000..13e4b2a
--- /dev/null
+++ b/debian/bin/igv
@@ -0,0 +1,3 @@
+#!/bin/sh
+set -eu
+exec java -jar /usr/share/java/igv.jar "$@"
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..e2d6f24
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+igv (1.4.2-1) UNRELEASED; urgency=low
+
+ * Initial release. Closes: #585457.
+
+ -- Shaun Jackman <sjackman at debian.org> Sun, 06 Jun 2010 12:41:59 -0700
diff --git a/debian/clean b/debian/clean
new file mode 100644
index 0000000..837e84b
--- /dev/null
+++ b/debian/clean
@@ -0,0 +1 @@
+igv.jar
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..7f8f011
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+7
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..c577912
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,28 @@
+Source: igv
+Section: non-free/science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Shaun Jackman <sjackman at debian.org>
+Build-Depends: ant, openjdk-6-jdk, debhelper (>= 7.0.50~),
+ junit4, libcommons-math-java, libconcurrent-java, libjargs-java,
+ libjhdf5-java, libjlibeps-java, liblog4j1.2-java, libsam-java,
+ libswing-layout-java
+Standards-Version: 3.8.4
+Homepage: http://www.broadinstitute.org/igv/
+Vcs-Git: git://git.debian.org/git/debian-med/igv.git
+Vcs-Browser: http://git.debian.org/?p=debian-med/igv.git
+
+Package: igv
+Architecture: any
+Depends: openjdk-6-jre, ${shlibs:Depends}, ${misc:Depends},
+ junit4, libcommons-math-java, libconcurrent-java, libjargs-java,
+ libjhdf5-java, libjlibeps-java, liblog4j1.2-java, libsam-java,
+ libswing-layout-java
+Description: Integrative Genomics Viewer
+ The Integrative Genomics Viewer (IGV) is a high-performance
+ visualization tool for interactive exploration of large, integrated
+ datasets. It supports a wide variety of data types including sequence
+ alignments, microarrays, and genomic annotations.
+ .
+ To cite your use of IGV, please reference http://www.broadinstitute.org/igv.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..91d6df6
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,27 @@
+Format-Specification: http://svn.debian.org/wsvn/dep/web/deps/dep5.mdwn?op=file&rev=135
+Name: GMAP
+Maintainer: igv-help at broadinstitute.org
+Source: http://www.broadinstitute.org/igv
+
+Copyright: 2009 The Broad Institute, Inc. and the Massachusetts Institute of Technology
+License: LGPL-2.1
+ See `/usr/share/common-licenses/LGPL-2.1'.
+
+Files: src/org/broad/igv/tdf/LEDataInputStream.java
+Copyright 1998-2009 Roedy Green, Canadian Mind Products
+License: other
+ This software may be copied and used freely for any purpose but
+ military. For explanatory text see
+ `http://mindprod.com/contact/nonmil.html'.
+
+Files: src/org/j3d/io/EndianConverter.java
+Copyright: 2001, 2002 Dipl. Ing. P. Szawlowski
+License: LGPL-2.1
+ See `/usr/share/common-licenses/LGPL-2.1'.
+
+Files: debian/*
+Copyright: 2010 Shaun Jackman <sjackman at debian.org>
+License: ISC
+ Permission to use, copy, modify, and/or distribute this software for any
+ purpose with or without fee is hereby granted, provided that the above
+ copyright notice and this permission notice appear in all copies.
diff --git a/debian/igv.1 b/debian/igv.1
new file mode 100644
index 0000000..376a494
--- /dev/null
+++ b/debian/igv.1
@@ -0,0 +1,24 @@
+.TH IGV "1" "June 2010" "IGV 1.4.2" "User Commands"
+.SH NAME
+igv \- Integrative Genomics Viewer
+.SH SYNOPSIS
+.B igv
+.br
+or
+.br
+\fBjava\fR -jar /usr/share/java/igv.jar
+.SH DESCRIPTION
+The Integrative Genomics Viewer (IGV) is a high-performance
+visualization tool for interactive exploration of large, integrated
+datasets. It supports a wide variety of data types including sequence
+alignments, microarrays, and genomic annotations.
+
+To cite your use of IGV, please reference
+ http://www.broadinstitute.org/igv
+.SH "REPORTING BUGS"
+igv-help at broadinstitute.org
+.SH COPYRIGHT
+Copyright 2009 The Broad Institute, Inc. and the Massachusetts
+Institute of Technology
+.SH "SEE ALSO"
+http://www.broadinstitute.org/igv/
diff --git a/debian/install b/debian/install
new file mode 100644
index 0000000..1ae2346
--- /dev/null
+++ b/debian/install
@@ -0,0 +1,2 @@
+debian/bin/* usr/bin
+igv.jar usr/share/java
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..648141f
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/igv.1
diff --git a/debian/patches/debian-changes-1.4.2-1 b/debian/patches/debian-changes-1.4.2-1
new file mode 100644
index 0000000..d3450bc
--- /dev/null
+++ b/debian/patches/debian-changes-1.4.2-1
@@ -0,0 +1,80 @@
+Description: Upstream changes introduced in version 1.4.2-1
+ This patch has been created by dpkg-source during the package build.
+ Here's the last changelog entry, hopefully it gives details on why
+ those changes were made:
+ .
+ igv (1.4.2-1) UNRELEASED; urgency=low
+ .
+ * Initial release. Closes: #585457.
+ .
+ The person named in the Author field signed this changelog entry.
+Author: Shaun Jackman <sjackman at debian.org>
+Bug-Debian: http://bugs.debian.org/585457
+
+---
+The information above should follow the Patch Tagging Guidelines, please
+checkout http://dep.debian.net/deps/dep3/ to learn about the format. Here
+are templates for supplementary fields that you might want to add:
+
+Origin: <vendor|upstream|other>, <url of original patch>
+Bug: <url in upstream bugtracker>
+Bug-Debian: http://bugs.debian.org/<bugnumber>
+Forwarded: <no|not-needed|url proving that it has been forwarded>
+Reviewed-By: <name and email of someone who approved the patch>
+Last-Update: <YYYY-MM-DD>
+
+--- igv-1.4.2.orig/build.xml
++++ igv-1.4.2/build.xml
+@@ -6,7 +6,7 @@
+
+ <!-- Source and lib directories -->
+ <property name="src.dir" value="${basedir}/src/" />
+- <property name="lib.dir" value="${basedir}/lib/" />
++ <property name="lib.dir" value="/usr/share/java/" />
+
+ <!-- Platform specific input files -->
+ <property name="native.dir" value="${basedir}/native/" />
+@@ -54,27 +54,25 @@
+ <!-- Create class path for manifest -->
+ <path id="@jars">
+ <pathelement path="${lib.dir}AbsoluteLayout.jar" />
+- <pathelement path="${lib.dir}ATV-3.1.jar" />
+ <pathelement path="${lib.dir}colt.jar" />
+ <pathelement path="${lib.dir}commons-math-1.1.jar" />
+ <pathelement path="${lib.dir}concurrent.jar" />
+ <pathelement path="${lib.dir}jargs.jar" />
+ <pathelement path="${lib.dir}jhdf5.jar" />
+- <pathelement path="${lib.dir}jhdf.jar" />
+- <pathelement path="${lib.dir}jibble.jar" />
++ <pathelement path="${lib.dir}net.sourceforge.jlibeps.jar" />
+ <pathelement path="${lib.dir}jide-action.jar" />
+ <pathelement path="${lib.dir}jide-common.jar" />
+ <pathelement path="${lib.dir}jide-components.jar" />
+ <pathelement path="${lib.dir}jide-dialogs.jar" />
+ <pathelement path="${lib.dir}jide-dock.jar" />
+ <pathelement path="${lib.dir}jide-grids.jar" />
+- <pathelement path="${lib.dir}junit-4.5.jar" />
++ <pathelement path="${lib.dir}junit4.jar" />
+ <pathelement path="${lib.dir}jlfgr-1_0.jar" />
+ <pathelement path="${lib.dir}ledatastream.jar" />
+- <pathelement path="${lib.dir}log4j-1.2.15.jar" />
++ <pathelement path="${lib.dir}log4j-1.2.jar" />
+ <pathelement path="${lib.dir}maf.jar" />
+- <pathelement path="${lib.dir}sam-1.08.jar" />
+- <pathelement path="${lib.dir}swing-layout-1.0.jar" />
++ <pathelement path="${lib.dir}sam.jar" />
++ <pathelement path="${lib.dir}swing-layout.jar" />
+ </path>
+
+ <pathconvert property="class-path" pathsep=" " dirsep="/" refid="@jars">
+--- igv-1.4.2.orig/src/org/broad/igv/ui/util/GenericUtilities.java
++++ igv-1.4.2/src/org/broad/igv/ui/util/GenericUtilities.java
+@@ -27,7 +27,7 @@ package org.broad.igv.ui.util;
+
+ import org.apache.log4j.Logger;
+ import org.broad.igv.IGVConstants;
+-import org.jibble.epsgraphics.EpsGraphics2D;
++import org.sourceforge.jlibeps.epsgraphics.*;
+
+ import javax.imageio.ImageIO;
+ import javax.swing.filechooser.FileFilter;
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..45d13b2
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+debian-changes-1.4.2-1
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..9ae5268
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,6 @@
+#!/usr/bin/make -f
+
+export DH_OPTIONS
+
+%:
+ dh $@
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
new file mode 100644
index 0000000..d2abaa6
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,2 @@
+version=3
+http://www.broadinstitute.org/igvdata/downloads/IGVDistribution_([1-9.]*)\.zip
--
Integrative Genomics Viewer
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