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

Shaun Jackman sjackman at gmail.com
Thu Jun 24 19:49:32 UTC 2010 

Hi James,

What is the copyright and license of maf.jar? Is there any documentation for it?

Cheers,
Shaun

On 17 June 2010 17:00, Shaun Jackman <sjackman at gmail.com> wrote:
> Hi James,
>
> I've removed support for MAF files from IGV. It was very straight
> forward and only required modifying to Java files and the build.xml
> file. Getting closer... the list of unresolved dependencies is now:
>
> AbsoluteLayout.jar      netbeans-platform
> jlfgr-1_0.jar   http://java.sun.com/developer/techDocs/hi/repository/
> ledatastream.jar        http://mindprod.com/products1.html#LEDATASTREAM
> colt.jar        http://acs.lbl.gov/software/colt/
> JIDE    http://www.jidesoft.com/
>
> Cheers,
> Shaun
>
> On 17 June 2010 11:15, James Robinson via RT
> <igv-help at broadinstitute.org> wrote:
>> Yes, removing support is an option,  its only used for the UCSC human
>> multiple alignments track,  a very rarely used option.
>>
>> ledatastream.jar comes from here
>>
>> http://mindprod.com/products1.html#LEDATASTREAM
>>
>>
>>
>> On Jun 17, 2010, at 2:02 PM, Shaun Jackman via RT wrote:
>>
>>>
>>> <URL: https://rt.broadinstitute.org/Ticket/Display.html?id=134078 >
>>>
>>> Hi Jim,
>>>
>>> Debian is divided up into its main repository and a non-free
>>> repository. Without source code, maf.jar could be packaged in the
>>> non-free repository, but it's definitely preferred to have the source
>>> code. Packaging other libraries requires additional work that would
>>> delay getting IGV into Debian. In the mean time, I could remove
>>> support for the MAF file format from IGV. Looking at
>>> TrackManager.java(load), it would be straight forward.
>>>
>>> That leaves ledatastream.jar and colt.jar to be resolved. I'll talk to
>>> the Debian-Java packaging team and see if they would be interested in
>>> packaging Colt.
>>>
>>> Cheers,
>>> Shaun
>>>
>>> On 16 June 2010 17:32, James Robinson via RT
>>> <igv-help at broadinstitute.org> wrote:
>>>> Hi,
>>>>
>>>> I'll look into a netbeans 6 port but it will be post release 1.5,
>>>> everything has gone through tests and is ready for release and I
>>>> don't
>>>> have time to go thought that process again.   Do you really have to
>>>> have source to do a debian package?   The developer of maf.jar is
>>>> very
>>>> busy and no its not actively maintained as a separate jar,  I
>>>> carefully carved that out from the predecessor to siphy.   The siphy
>>>> route might be the only option if you must have source.
>>>>
>>>> Jim
>>>>
>>>>
>>>> On Jun 16, 2010, at 8:24 PM, Shaun Jackman via RT wrote:
>>>>
>>>>>
>>>>> <URL: https://rt.broadinstitute.org/Ticket/Display.html?id=134078 >
>>>>>
>>>>> Hi Jim,
>>>>>
>>>>> For AbsoluteLayout, NetBeans version 6 doesn't seem to provide
>>>>> AbsoluteConstraints. I know naught about NetBeans, but it looks as
>>>>> though you're meant to use the member functions
>>>>> childWidget.getPreferredLocation and childWidget.getPreferredBounds
>>>>> rather than AbsoluteConstraints:
>>>>> http://bits.netbeans.org/dev/javadoc/org-netbeans-api-visual/org/netbeans/api/visual/widget/doc-files/documentation.html#AbsoluteLayout
>>>>>
>>>>> Would you be able to port IGV to NetBeans 6?
>>>>>
>>>>> For maf.jar, I'd need the source code (and its license) to be able
>>>>> to
>>>>> package it for Debian. It would be best if I had a web page that I
>>>>> could point to, but it's not strictly necessary. An e-mail address
>>>>> of
>>>>> a contact would be good. Is maf.jar still actively maintained?
>>>>>
>>>>> Cheers,
>>>>> Shaun
>>>>>
>>>>> On 16 June 2010 16:08, James Robinson via RT
>>>>> <igv-help at broadinstitute.org> wrote:
>>>>>> I'm very involved in the HDF5 discussion and with Dana Robinson
>>>>>> behind
>>>>>> the scenes.   Heng Li and I will be meeting Dana when he's in
>>>>>> Boston
>>>>>> next month.  We're going to collaborate on IGV support for their
>>>>>> alignment format.   I doubt very much that there will be any
>>>>>> significant performance advantage over BAM when the full spec is
>>>>>> supported,  but I'm neutral on this and will support both if/when
>>>>>> they
>>>>>> have something.
>>>>>>
>>>>>> TDF is IGV's binary format,   similar to bigWIG but it supports
>>>>>> more
>>>>>> formats (all the IGV formats).
>>>>>>
>>>>>> The main reason for the port was (1) performance, and (2) the
>>>>>> lack of
>>>>>> pure java readers.  The performance issue has to do with the
>>>>>> details
>>>>>> of the hierarchical data model IGV uses,  HDF5 wasn't a good fit.
>>>>>> The lack of native java support was significant,  requiring JNI and
>>>>>> builds for every OS / Architecture combination,  basically an
>>>>>> intractable problem for a platform independent tool like IGV.   It
>>>>>> negated Java's advantage in that regard.
>>>>>>
>>>>>> RE AbsoluteLayout,  that should be compatible,  its probably just a
>>>>>> later version of the jar I'm using.    You are free to package
>>>>>> maf.jar,  do you need a webpage or reference to do that?  Its an
>>>>>> internal library used here,  it doesn't have a webpage and probably
>>>>>> never will.
>>>>>>
>>>>>> Jim
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Jun 16, 2010, at 6:05 PM, Shaun Jackman via RT wrote:
>>>>>>
>>>>>>>
>>>>>>> <URL: https://rt.broadinstitute.org/Ticket/Display.html?
>>>>>>> id=134078 >
>>>>>>>
>>>>>>> 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
>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>
>>
>>
>

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