[Debian-med-packaging] [rt.broad #134078] Packaging IGV for Debian [PATCH]

[Shaun Jackman]

Hi James,

What is TDF? I haven't heard of it. Why did you migrate from HDF5?
There's a discussion on the samtools mailing list right now about
whether BAM should be adapted to HDF5. HDF5 is in Debian. So it's not
an issue.

Debian does have batik (libbatik-java), so that's good.

The Debian package netbeans-platform contains a class named AbsoluteLayout
org.netbeans.modules.visual.layout.AbsoluteLayout
Do you know whether this class would be compatible with IGV? It's in a
different package than the one used by IGV:
org.netbeans.lib.awtextra.AbsoluteLayout

maf.jar seems to be included with siphy, but I couldn't find a web
page for just maf.jar. Does it have a web page? I'd rather just
package maf.jar rather than all of siphy.

Cheers,
Shaun

On 16 June 2010 11:10, James Robinson via RT
<igv-help at broadinstitute.org> wrote:
>
> Hi Shaun,
>
> Thanks for doing this work!  And also for the H5 tip.   I'll include
> this change in the upcoming 1.5 release (early next week).   HDF5 is
> included only for legacy purposes,  and will be dropped soon,
> probably in the release after 1.5.   Originally that was the IGV
> binary format but it was replaced by TDF a year ago.
>
> The components you mention are neccessary,  AbsoluteLayout.jar is used
> for window layouts,  colt.jar is used for computing percentiles,
> ledatastream is used for reading little-endian file formats,
> including TDF,  and maf.jar is used for reading multiple alignment
> files.  The maf.jar file is from another group here at the Broad.
>
> In 1.5 I have dropped jibble.jar in favor of the apache-commons
> "batik" package (http://xmlgraphics.apache.org/batik/).   The bad news
> is there is a slew of jars included with this package.   Do you know
> if its part of the debian distribution?
>
> Jim
>
>> 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;
>>
>>
>
>
>