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Old 03-03-2014, 06:00 PM   #1
Dr_Funkenstein
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Location: North Carolina USA

Join Date: Dec 2013
Posts: 2
Default Amazon Web Services: Tophat cannot find Bowtie2 even though Bowtie2 is in path

Hi there,

This is quite vexing, Bowtie2 is in my path but Tophat complains that it is not on the system.

I am using Amazon Linux, 64-bit and I installed binaries of Tophat, Bowtie and cufflinks. Samtools was compiled from source code.

.bash_profile has the following:
TUX_PATH=/home/ec2-user/software
PATH=$PATH:$TUX_PATH/bowtie:$TUX_PATH/cufflinks:$TUX_PATH/tophat:$TUX_PATH/samtools
export PATH


Typing "bowtie2 --version" from any subdirectory yields:
/home/ec2-user/software/bowtie/bowtie2-align-s version 2.2.1
64-bit
Built on igm2


Likewise, Tophat, Cufflinks and Samtools are all found from any subdirectory.

However, running TopHat using a script that works fine on my own Linux box at home yields:
Checking for Bowtie
Bowtie 2 not found, checking for older version..
Error: Bowtie not found on this system.


I'm at my wits end here.

Thanks,
Dr Funkenstein
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Old 03-03-2014, 06:23 PM   #2
GenoMax
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Location: East Coast USA

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Do bowtie2 script and executables have execute permissions for all?
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Old 03-03-2014, 06:36 PM   #3
fpr
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Location: East US

Join Date: Apr 2012
Posts: 5
Default

you should run env (or similar) insider your script to make sure that the PATH and other environment variables poins to the places you think they should be pointing. The next thing will be checking that the permission are right (executable for the right user/group etc).
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Old 03-05-2014, 12:51 PM   #4
westerman
Rick Westerman
 
Location: Purdue University, Indiana, USA

Join Date: Jun 2008
Posts: 1,104
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The latest version of Bowtie2 does not work with the 2nd-to-last-version of Tophat (the latest was released 03-04-2013 ... after your post). See the tophat home page:

http://tophat.cbcb.umd.edu/

I suspect that this is your problem. Solution: use an older version of Bowtie2 or upgrade to the 03-04 version of Tophat (I have not tried out the latter solution).
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Old 03-06-2014, 04:55 AM   #5
Dr_Funkenstein
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Location: North Carolina USA

Join Date: Dec 2013
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Westerman,

You are absolutely correct !! When I installed Bowtie 1 - all is happy. I will play around with Tophat and Bowtie until I get a reasonably up-to-date pair.

Thanks again !!!
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