I'm confused. So I installed tophat-2.0.6.Linux_x86_64 which seems to contain tophat and tophat2. Can't galaxy use that tophat? Am I supposed to also install tophat 1? Does galaxy somehow failover to use tophat2 otherwise? What am I missing? Thanks, Greg On Thu, Dec 13, 2012 at 2:32 PM, Jeremy Goecks <jeremy.goecks@emory.edu> wrote:

On Dec 13, 2012, at 2:13 PM, greg wrote:

...

I'm seeing the error below when I try to run Tophat for Illumina.

Has anyone seen this before? Could I have installed bowtie incorrectly or am I simply running with the wrong data/parameters?

You are using Tophat2, not Tophat (note the version at the beginning of the log). You can either

(a) install and use Tophat 1.X

or

(b) use the Tophat2 wrapper in conjunction with Bowtie2.

For (a), you'll want to modify the bowtie_indices.loc; for (b), modify bowtie2_indices.loc

J.

...

Thanks,

Greg

(I'm also really confused why the error is mentioned /tmp/* paths. I never assigned anything to /tmp in the universe_wsgi.ini. Where is it getting that from?)

Error in tophat:

[2012-12-13 13:55:01] Beginning TopHat run (v2.0.6) ----------------------------------------------- [2012-12-13 13:55:01] Checking for Bowtie Bowtie version: 2.0.2.0 [2012-12-13 13:55:01] Checking for Samtools Samtools version: 0.1.18.0 [2012-12-13 13:55:01] Checking for Bowtie index files Error: Could not find Bowtie 2 index files (/tmp/4036894.1.f04.q/tmp4TrEQQ/dataset_75.*.bt2) ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:

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