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.
> 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.
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