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Question: Tophat
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gravatar for Luciano Cosme
7.3 years ago by
Luciano Cosme • 220
Luciano Cosme • 220 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
alignment bowtie samtools bam • 1.4k views
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modified 7.3 years ago by Jennifer Hillman Jackson ♦ 25k • written 7.3 years ago by Luciano Cosme • 220
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gravatar for Jennifer Hillman Jackson
7.3 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:
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 -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support
ADD COMMENT • link written 7.3 years ago by Jennifer Hillman Jackson ♦ 25k
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