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
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@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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