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

[Tony Travis]

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




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