Thanks for the quick answer. Could access bowtie2 from command line without a 
problem. Found that I had to include a line pointing to the wrapper in 
tool_conf.xml. It wasn't there by default. 
Now two new problems:

- bowtie2 does not show any built-in reference genomes

- when I try to import a file from EBI-SRA (I paste the ftp address into 
"Upload File") it's loading without stopping until the drive is full (>97 GB), 
although the file itself is only about 3GB. Is it a problem with the EBI server 
or within galaxy?

Thanks for any help. 


On Oct 14, 2013, at 5:50 PM, Vipin TS wrote:

> Hi Stanislas, 
> 
> Please check the PATH variable and make sure that you can access bowtie2 from 
> command line and then restart the Galaxy service through cloudman interface. 
> I think that should work. 
> 
> Vipin
>  
> 
> I'm trying to run Galaxy on an Amazon AWS cloud using the normal Cloudman 
> distribution (ami-118bfc78). The instatiated Galaxy however does not contain 
> Bowtie2 and Tophat2, even after updating through the Cloudman Admin section. 
> Although the wrappers are there in the tools directory, when I access it 
> through ssh. I've also installed Bowtie2 manually on the server and the 
> command bowtie2 does get recognized.
> How cat I get these two to run on the Galaxy instance?
> 
> Thanks for your help.
> Best
> Stanislas
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