Hi Sarah,

i looks like something is wrong with the PBS system.
The errors for bedtools and repeatmasker are the same. I can't
understand french but i guess that ";" are not supported by PBS or in
your configuration? Repeatmasker and bedtools creating more than one
shell command and concatenating them with ';'.

Hope that helps,
Bjoern

> Hello,
> 
> I've installed NEBULA tools and "RepeatMasker" tool on our local
> Galaxy instance.
> 
> For some tools (others work), I get the following errors:
> - Here is the error I get when running the tool FilterControl 
> *** glibc detected *** java: double free or corruption (!prev): 
> 0x00007fe56800ecd0 ***
> *** glibc detected *** java: double free or corruption (!prev): 
> 0x00007fe56800ecd0 ***
> *** glibc detected *** java: double free or corruption (!prev): 
> 0x00007fe56800ecd0 ***
> *** glibc detected *** java: double free or corruption (!prev): 
> 0x00007fe56800ecd0 ***
> /usr/local/bioinfo/src/galaxy/galaxy-dist/tools/Nebula/FilterControlPeaks/FilterControlPeaks.sh:
>  line 80: 61310 Abandon                 java -classpath $LOCAL_PATH/ -Xmx6g 
> FilterPeaks -f $inputfile -c $controlfile -t $minHeight -v $minRatio -o 
> $output > /dev/null
> *** glibc detected *** java: double free or corruption (!prev): 
> 0x00007f1f5800ecd0 ***
> /usr/local/bioinfo/src/galaxy/galaxy-dist/tools/Nebula/FilterControlPeaks/FilterControlPeaks.sh:
>  line 81: 61351 Abandon      
> 
> - Here is the error I get when running the tool IntersectBed 
> 
> /work/galaxy/database/pbs/galaxy_4129.sh: line 13: Erreur de syntaxe
> près du symbole inattendu « ;; »
> /work/galaxy/database/pbs/galaxy_4129.sh: line 13: `bedtools intersect
> -f 0.05
> 
> - Here is the error I get when running the tool ChIPmunk (thanks Alban
> for you help (ChIPMunk v2 is used and all librairies are found) but
> here is a new error, maybe a problem of "dirname" ?)
> 
> mv: impossible d'évaluer
> « 
> /work/galaxy/database/job_working_directory/004/4132/galaxy_dataset_5992.dat_0.xml.png
>  »: Aucun fichier ou dossier de ce type
> mv: impossible d'évaluer « /work/gala
> 
> 
> - Here is the error I get when running the tool PeaksToBed 
> readline() on closed filehandle FILE at
>       
> /usr/local/bioinfo/src/galaxy/galaxy-dist/tools/Nebula/Peak2Bed/peak2bed.pl 
> line 124 (#1)
>     (W closed) The filehandle you're reading from got itself closed sometime
>     before now.  Check your control flow.
>     
> Use of uninitialized value $fields[1] in concatenation (.) or string at
>       
> /usr/local/bioinfo/src/galaxy/galaxy-dist/tools/Nebula/Peak2Bed/peak2bed.pl 
> line 154, <FILE> line 1 (#2)
>     (W uninitialized) An undefined value was used as if it were already
>     defined.  It was interpreted as a "" or a 0, but maybe it was a mistake.
>     To suppress this warning assign a defined value to your variables.
>     
>     To help you figure out what was undefined, perl will try to tell you the
>     name of the variable (if any) that was undefined. In some cases it cannot
>     do this, so it also tells you what operation you used the undefined value
>     in.  Note, however, that perl optimizes your program and the operation
>     displayed in the warning may not necessarily appear literally in your
>     program.  For example, "that $foo" is usually optimized into "that "
>     . $foo, and the warning will refer to the concatenation (.) operator,
>     even though there is no . in your program.
>     
> Use of uninitialized value in concatenation (.) or string at
>       
> /usr/local/bioinfo/src/galaxy/galaxy-dist/tools/Nebula/Peak2Bed/peak2bed.pl 
> line 154, <FILE> line 1 (#2)
> Use of uninitialized value in numeric ge (>=) at
>       
> /usr/local/bioinfo/src/galaxy/galaxy-dist/tools/Nebula/Peak2Bed/peak2bed.pl 
> line 156, <FILE> line 1 (#2)
> ......
>       
> /usr/local/bioinfo/src/galaxy/galaxy-dist/tools/Nebula/Peak2Bed/peak2bed.pl 
> line 156, <FILE> line 63 (#2)
> 
> Use of uninitialized value $fields[1] in conc
> 
> 
> I dowloaded tool "RepeatMasker" from Galaxy Tool Shed,and RepeatMasker
> is installed on our cluster.
> Here is the error I get when running the tool RepeatMasker:
> 
> An error occurred running this job: Epilog : job finished at jeu.
> janv. 31 14:39:16 CET 2013
> /work/galaxy/database/pbs/galaxy_4134.sh: line 13: Erreur de syntaxe
> près du symbole inattendu « ;; »
> /work/galaxy/database/pbs/galaxy_4134.sh: line 13: `RepeatMasker
> -parallel 8 -speci
> 
> 
> Do you have any ideas ?
> Thank you in advance for your help,
> Sarah Maman 
> -- 
>           --*--
> Sarah Maman
> INRA - LGC - SIGENAE
> http://www.sigenae.org/
> Chemin de Borde-Rouge - Auzeville - BP 52627
> 31326 Castanet-Tolosan cedex - FRANCE
> Tel:   +33(0)5.61.28.57.08
> Fax:   +33(0)5.61.28.57.53 
>          --*--

-- 
Björn Grüning
Albert-Ludwigs-Universität Freiburg
Institute of Pharmaceutical Sciences
Pharmaceutical Bioinformatics
Hermann-Herder-Strasse 9
D-79104 Freiburg i. Br.

Tel.:  +49 761 203-4872
Fax.:  +49 761 203-97769
E-Mail: bjoern.gruen...@pharmazie.uni-freiburg.de
Web: http://www.pharmaceutical-bioinformatics.org/

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