Hi,
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 >
./tophat_out/tmp/dataset_26.dat.fa
[Fri Jul 29 17:56:39 2011] Checking for Bowtie
Bowtie version: 0.12.7.0
[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.
Luciano
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