[galaxy-dev] Tophat for Illumina Error: Could not find Bowtie 2 index files

2012-12-13 Thread greg 
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?

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)
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Re: [galaxy-dev] Tophat for Illumina Error: Could not find Bowtie 2 index files

2012-12-13 Thread greg 
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.goe...@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)
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Re: [galaxy-dev] Tophat for Illumina Error: Could not find Bowtie 2 index files

2012-12-13 Thread Jeremy Goecks 

 I'm confused.  So I installed tophat-2.0.6.Linux_x86_64 which seems to
 contain tophat and tophat2.  

tophat2 redirects to tophat, which is tophat version 2.X.X

 Can't galaxy use that tophat?

You can, but you need to use the Tophat2 wrapper, not the Tophat for Illumina 
wrapper. And, when you use the Tophat2 wrapper, you'll need to have Bowtie2 
installed and the bowtie2_indices.loc set up appropriately.

J.
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