[Debian-med-packaging] Packaging IGV for Debian [PATCH]

[Shaun Jackman]

Hi,

I'm interested in packaging IGV for Debian as part of the Debian Med
project. Resolving the dependencies of IGV is ongoing work, but many
of the dependencies are already packaged for Debian. These
dependencies are unresolved:
AbsoluteLayout.jar
colt.jar
JIDE
ledatastream.jar
maf.jar

Could you comment on whether each of these is a necessary component of
IGV, or which could potentially be removed?

Debian does not package Jibble, but it does package the GPL-licensed
jlibeps, which is a drop-in replacement:
http://jlibeps.sourceforge.net/

A single line change is needed for the source code to use jlibeps. See
the patch following this e-mail.

I had trouble compiling this line:
    dataType = H5.H5Tcopy(H5.J2C(HDF5Constants.H5T_C_S1));
        After reading some HDF5 documentation, I found that it is
unnecessary to call J2C for a constant beginning with the prefix H5,
as both the Java and C constant have the same value:
http://www.ssec.wisc.edu/visad-docs/javadoc/ncsa/hdf/hdf5lib/HDF5CDataTypes.html

Cheers,
Shaun

--- igv-1.4.2.orig/src/org/broad/igv/h5/HDF5LocalWriter.java
+++ igv-1.4.2/src/org/broad/igv/h5/HDF5LocalWriter.java
@@ -491,7 +491,7 @@ public class HDF5LocalWriter implements
                 buf =
                         new double[]{((Number) value).doubleValue()};
             } else {
-                dataType = H5.H5Tcopy(H5.J2C(HDF5Constants.H5T_C_S1));
+                dataType = H5.H5Tcopy(HDF5Constants.H5T_C_S1);
                 buf =
                         value.toString().getBytes();
                 H5.H5Tset_size(dataType, ((byte[]) buf).length);
--- 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;