Hello Luciano,

Here are is the core wiki link to help with NGS tools (including SamTools) set up and installation.


http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup

For next time, the galaxy-...@bx.psu.edu mailing list would be the best place to send new questions or even follow-up questions to this one if problems persist. The development community can be very helpful in sorting out local installation issue that may come up. Subscribing may also be of interest:
http://lists.bx.psu.edu/listinfo/galaxy-dev
http://galaxyproject.org/Support

Thanks!

Jen
Galaxy team

On 8/1/11 8:53 AM, Luciano Cosme wrote:
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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