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-dev(a)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
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at
usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/Support