> - bowtie2 does not show any built-in reference genomes
>
>
by default Cloudman didn't ship the genome index for bowtie2. Bowtie2 use
its own index set.
Usage: bowtie2-build [option] genome.fa index_basename

and add the entries in "bowtie2_indices.loc". Please make sure that the fields
are tab delimited,
not space delimited, and have no trailing or extra whitespace (this is easy
to slip in by accident).
and place the *.loc file under /mnt/galaxyIndices/galaxy/tool-data/

Most of the genome reference file are located at base folder:
/mnt/galaxyIndices/genomes/

example:
/mnt/galaxyIndices/genomes/Athaliana/araTha_tair9/seq/Arabidopsis_thaliana.TAIR9.55.dna.toplevel.fa.gz



> - 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?
>

I am not sure, can you please paste the url which points to the file.



>
> 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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>
>
>
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