Le 11/8/12 11:08 AM, Andreas Tille a écrit :
> On Thu, Nov 08, 2012 at 09:26:27AM +0100, Olivier Sallou wrote:
>>> uk/ac/babraham/FastQC/FastQCApplication.class is missing in the jar file
>>> /usr/share/fastqc/fastqc.jar (you can check content with jar -tf
>>> /usr/share/fastqc/fastqc.jar)
>> To get it work, you should fix the /usr/bin/fastq line 183 on exec to get:
>>
>> exec $java_bin,@java_args,"-jar","/usr/share/fastqc/fastqc.jar", @files;
>>
>> instead of
>>
>> exec $java_bin,@java_args, "uk.ac.babraham.FastQC.FastQCApplication",
>> @files;
>
> This sounds somehow obvious and works (even if I wonder why my manual
> call at command line which exactly did what you suggested was (and is)
> failing).
It seems that the exec call loose the ENV{CLASSPATH} set by the perl
program where dependencies are set. As classpath is correctly set in the
manifest, calling the -jar works perfectly.
If you call on command line: java -cp
/usr/share/fastqc/fastqc.jar:path_tobam.jar:path_to-bzip2.jar
uk.ac.babraham.FastQC.FastQCApplication, it works fine too.
> Thanks for your help
>
> Andreas.
>
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