Re: Help needed to update to latest fastqc

[Olivier Sallou <olivier.sallou@irisa.fr>]

After a quick look, there is a library issue (at least)

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).

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.

Olivier

On 05/03/2015 08:54 AM, Andreas Tille wrote:

Hi,

I tried to upgrade to the latest fasqc version.  When doing so I decided
to move from SVN to Git:

  Vcs-Git: git://anonscm.debian.org/debian-med/fastqc.git

Upstream needs a new Build-Depends libjhdf5-java which I added.
However, I was not able to fix the build.  When trying I considered
switching from the Makefile based build to ant (which sounds natural)
Unfortunately I did not succeeded in adapting build.xml.

Any help would be appreciated

     Andreas.

-- 
Olivier Sallou
IRISA / University of Rennes 1
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