Re: Help needed to update to latest fastqc
Hi Tim,
from my *very* naive point of view your considerations make sense.
Olivier might have some more educated opinion (and perhaps some code?).
I'll be available vor sponsering as usual.
Thanks for your work on this
Andreas.
On Wed, Aug 12, 2015 at 11:44:19AM +0100, 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:
>
> ---
>
> 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!
>
> 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.
>
> 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
> > >
> > > gpg key id: 4096R/326D8438 (keyring.debian.org)
> > > Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
> > >
> > >
> > > --
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> > >
> > >
> >
> > --
> > http://fam-tille.de
> >
> >
>
> --
> Nothing is inherently mysterious - nothing that actually exists, that
> is. If I am ignorant about a phenomenon, that is a fact about my state
> of mind, not a fact about the phenomenon; to worship a phenomenon
> because it seems so wonderfully mysterious, is to worship your own
> ignorance.
>
> - Eliezer Yudkowsky
>
>
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