[Bio-linux-dev] [Bio-Linux] problem running picard-tools under Bio-Linux

[Tim Booth]

Hi Tony,

Thanks for the report.  I've pushed a fix to the PPA just now but I've
not tested it as I was hoping you could give it a quick try for me once
it builds.  My basic tests for this package don't include any BZip2
files to try, which is why I missed the issue.

Regarding the fix, I don't want to add items to the classpath within the
shell script as I'd consider this a workaround for the underlying bug -
ie. that the JAR built by the upstream build.xml does not declare its
dependencies within its manifest properly.  I thought I'd sorted this
but I clearly missed out bzip2.jar in my original fix.


Cheers,

TIM

On Wed, 2013-10-16 at 16:30 +0100, Tony Travis wrote:
> Hi,
> 
> We've had problems running picard-tools under Bio-Linux 7 because the
> CLASSPATH was not set, and the wrapper script does not set -cp for the
> sam and bzip2 jars. It works if I set the java -cp paths explicity in
> the wrapper:
> 
> HTH,
> 
>   Tony.
> 
> > rwt017 at wildcat:~$ diff -Naur /usr/bin/picard-tools /usr/local/bin/test-picard-tools
> > --- /usr/bin/picard-tools     2013-08-16 14:45:04.000000000 +0100
> > +++ /usr/local/bin/test-picard-tools  2013-10-16 14:44:44.347312505 +0100
> > @@ -1,6 +1,6 @@
> >  #!/bin/sh
> >  set -eu
> > -if [ `basename -- $0` = picard-tools ]; then
> > +if [ `basename -- $0` = test-picard-tools ]; then
> >       if [ $# = 0 ]; then
> >               cat 1>&2 <<EOF
> >  picard-tools: missing command argument
> > @@ -56,4 +56,4 @@
> >
> >  # Note, jbzip2.jar and sam.jar etc. should now be added to cp implicitly
> >  p=/usr/share/java
> > -exec java -XX:MaxPermSize=256m -cp $p/picard.jar $main "$@"
> > +exec java -XX:MaxPermSize=256m -cp $p/picard.jar:sam.jar:$p/jbzip2.jar $main "$@"
> 
> --
> Dr. A.J.Travis, University of Aberdeen, Institute of Biological and
> Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen
> AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396
> http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis
> 
> 
> 
> 
> The University of Aberdeen is a charity registered in Scotland, No SC013683.
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-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
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OX10 8BB 

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