I tried both File1 and 2 of SRR618542. Here's one of the links:
On Oct 14, 2013, at 8:01 PM, Vipin TS wrote:
> - 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:
> - 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.
>> 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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