I am running galaxy locally and when I perform alignments with TopHat I
get the following error:

Error in tophat:

[Fri Jul 29 17:55:47 2011] Beginning TopHat run (v1.3.1)
[Fri Jul 29 17:55:47 2011] Preparing output location ./tophat_out/
[Fri Jul 29 17:55:47 2011] Checking for Bowtie index files
[Fri Jul 29 17:55:47 2011] Checking for reference FASTA file
        Warning: Could not find FASTA file /tmp/tmp1dXHLG/dataset_26.dat.fa
[Fri Jul 29 17:55:47 2011] Reconstituting reference FASTA file from Bowtie index
Executing: /bin/bowtie-inspect /tmp/tmp1dXHLG/dataset_26.dat >
[Fri Jul 29 17:56:39 2011] Checking for Bowtie
        Bowtie version:        
[Fri Jul 29 17:56:39 2011] Checking for Samtools
Error locating program: samtools

   I installed the samtools (in several places already), but it seems I did
not put it in the right place. So where galaxy search for it?
Thank you.

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