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 --*--

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