Re: Help needed to update to latest fastqc
On 08/12/2015 12:44 PM, Tim Booth wrote:
> Hi Andreas and Olivier,
>
> I'm going to have a crack at the FastQC update. I've been poking at the
> HDF5 packages and here are my conclusions so far:
I already had a look and started some work. In fact I expected to
progress on it during Debconf, but if you started it...
> ---
>
> We have 2 Free Java libraries for HDF5:
>
> 1) The "NCSA" lib distributed by hdfgroup.org with classes in namespace
> ncsa.hdf.hdf5lib, packaged on Debian as libjhdf5-java.
>
> 2) The "CISD" aka. "SIS" lib distributed by ethz.ch with classes in the
> namespace ch.systemsx, not currently packaged on Debian.
>
> The SIS library forks some Java code from the ncsa.hdf namespace, and
> also needs to link against the NCSA native library (via JNI) at runtime.
>
> So, trying to package sis-jhdf5:
>
> wget
> 'https://wiki-bsse.ethz.ch/download/attachments/26609237/sis-jhdf5-14.12.1-r33502.zip?version=1&modificationDate=1424599261225&api=v2'
> # The source is in a zip within the zip...
> unzip sis-*
> mkdir sis-jhdf5-14.12.1
> cd !$
> unzip ../sis-jhdf5/src/sis-jhdf5-src.zip
>
> For compilation to succeed, we also need sis-base, not to be confused
> with the entirely separate project at sis.apache.org!
Is it all ? In my previous check, it seemed (but not sure, it was quite
some time ago) that there were multiple dependencies (or sis-base itself
depending on other libs to package in sis repo)
>
> wget
> http://bs-svn01.ethz.ch/repos/cisd/libraries/trunk/sis-base/sis-base-src.zip
>
> The code also depends on their own args4j library, but only for the CLI
> under ch/systemsx/cisd/hdf5/h5ar/HDF5ArchiverMain.java which we can
> simply leave out just now.
>
> So - can we exclude the ncsa.hdf.hdf5lib.* classes from sis-jhdf5 and
> compile it against the existing classes in /usr/share/java/jhdf5.jar?
> My conclusion is not, because...
>
> The version of ncsa/hdf/hdf5lib/exceptions/HDF5Exception.java supplied
> with the sis-jhdf5 code subclasses RuntimeException but the version in
> libhdf5-java does not. The result is that the code here does not need
> to declare the exceptions being thrown, and thus simply ignores them
> all. One can go through and add all "throws" declarations (there are a
> _lot_ of them!!), but then any client code using the library will also
> break unless it is likewise patched or the code is modified to handle
> the exceptions internally. I think we'd best just admit defeat here and
> use the code supplied with sis-jhdf5.
I think that we should indeed keep the "copied" code from original, as I
think they adapted it for their needs. Makihng modifications to use
completly nca would make it unmaintainable in later updates I think.
>
> So, I'm going to try rolling two new packages, and see if that allows me
> to compile the latest FastQC:
>
> libsis-base-java (should be simple)
> libsis-jhdf5-java (depends on libsis-base-java + existing libjhdf5-jni)
>
> I'll report back on progress and commit to SVN as usual. Let me know if
> you think I'm missing something.
>
> Cheers,
>
> TIM
>
>
> On Thu, 2015-06-25 at 09:37 +0200, Andreas Tille wrote:
>> Hi Olivier,
>>
>> any news about this hdf5lib packaging?
>>
>> Kind regards
>>
>> Andreas.
>>
>> On Tue, May 05, 2015 at 09:25:23AM +0200, Olivier Sallou wrote:
>>>
>>> On 05/04/2015 10:52 PM, Andreas Tille wrote:
>>>> Hi Olivier,
>>>>
>>>> On Mon, May 04, 2015 at 06:41:10PM +0200, Olivier Sallou wrote:
>>>>> File fastqc/uk/ac/babraham/FastQC/Sequence/Fast5File.java imports
>>>>> HDFS5Factory from ch.systemsx.cisd.hdf5
>>>>>
>>>>> but jhdf5.jar only contains files like: ncsa/hdf/hdf5lib/... and no
>>>>> HDF5Factory
>>>>>
>>>>> this jhdf5 is not the correctl lib (or an other one is needed).
>>>> I guess its this one:
>>>>
>>>> https://svncisd.ethz.ch/doc/hdf5/hdf5-8.10/ch/systemsx/cisd/hdf5/package-summary.html
>>> seems that original code source is the same
>>> (https://svncisd.ethz.ch/repos/cisd/jhdf5/trunk/source/java/)
>>> (/ncsa/...) but that /ch/... has not been included for a reason
>>>>
>>>>> In addition, in debian/patches/build.xml is missing commons-math3.jar to
>>>>> be added in pathelement for classpath.
>>>>>
>>>>> for duplicate classes, I don't yet, but hdf5 first need to be resolved.
>>>> If I do not hear from you I'll try the URL above tomorrow (if nobody
>>>> else might beat me which would for sure welcome as always).
>>>>
>>>> Kind regards
>>>>
>>>> Andreas.
>>>>
>>> --
>>> Olivier Sallou
>>> IRISA / University of Rennes 1
>>> Campus de Beaulieu, 35000 RENNES - FRANCE
>>> Tel: 02.99.84.71.95
>>>
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>>>
>>>
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>> --
>> http://fam-tille.de
>>
>>
>
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