- 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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